Hi, this is Allison Sheridan of the NoCellicast podcast, hosted at podfeed.com, a technology geek podcast with an ever so slight Apple bias. Today is Sunday, April 9th, 2023, and this is show number 935. Well, I started doing an impromptu poll over in our Slack community, asking people whether they would like me to introduce the subjects that are gonna be in the podcast each week before I actually talk about them. The results were mixed, but one of the members said, you're asking the wrong people. You should find out whether it helps new people to the podcast if you do that. So I have a question to you, if you're new or even if you've been around for a while listening, do you like it when I tell you what's coming or would rather I just get to work and start the show? Again, like I said, the results have been mixed and I'm not sure which way we should go, so I'd like your opinion. So send me an email at alison at podfeed.com or hit me up on mastodon at podfeed.chaos.social. I always enjoy it when barbou shots has me on Let's Talk Apple, especially when I have them all to myself. Well, this week we got together and went over all the news about Apple in the month of March, including subjects like Apple and China and India. As he says, it's complicated. We talked about Apple Pay later launching and Bart explains why having a dedicated classical music app matters. I really didn't understand why we needed one. Anyway, you can find Let's Talk Apple in your podcatcher of choice or at letstalk.ie. Well, if you know that music, you know it's time for a tiny tip. And I had a tiny tip I've been sitting on for a long time that I was super excited about and I wrote it up as an article on podfeed.com and after I posted it, Yope came in with a comment that explains a way easier tiny tip to fix the problem. But I'm gonna tell you my tiny tip first and then I'll follow up with the way Yope says to do it, which like I said, it's way better than mine. Mine's kind of cool, but his is probably more elegant. All right, here's the setup. When you're using an app that expects long-winded typing on iOS, you'll get the standard iOS keyboard with four rows of keys. On the fourth row of an American English keyboard, you'll find a key labeled return. Hitting this key gives you a line feed, which is an expected feature for separating long thoughts for readability. However, short form apps like, say, Mastodon, Discord and Twitter use a different keyboard layout that replaces the return key with two keys, the at and hashtag symbols. To be fair, those are pretty darn useful keys to have at your fingertips in this kind of app and I bet most people would prefer having access to them versus having access to a return key if they had to make a choice. However, when I'm sending a link through one of these apps on, like I said, Mastodon, Discord or Twitter, I think it's nice to say something about the link first to get people motivated to actually click it and then I put in a couple of line feeds to separate the text from the link and so then I paste the link. This sets it off nicely and makes it easier for your followers to read. Our tiny tip for today is how to add a line feed when there is no return key on the keyboard. It's super easy. Hit the microphone in the bottom right to enable dictation and say, new line, easy peasy. Well, like I said, after I wrote up this post, Yope, who's also known on Mastodon as Owit Grunin at mstdn.social and I've got a link in the show notes, of course, Yope wrote a comment below with an even better solution. If you don't see a return key, look in the bottom left of the keyboard. You should see a key with one, two, three on it. Tap the key once and the keyboard will change to show you all of the numbers and special characters. I've seen this before, I use it all the time but it turns out it also changes the bottom right key back into a return key. I can't believe I never noticed that it was doing this when I switched between the alpha keys and the number keys. It's a great solution and this is a good illustration of how great it is to be part of such a vibrant community and I can learn something when I thought I was teaching something. Thank you so much, Yope, for this second tiny tip. Hello, this is Jill from the Northwoods. The story of me buying an iPad goes all the way back to 2010. I was in charge of a pool of medical tablets for medical staff to carry around and enter in patient information through these tablets and I meant to keep them healthy. I would give them out when there were certain types of demonstrations that required them, keep them updated, all that. And I just had dreamed of the day when I could have such an amazing device. And then in March of 2010, the iPad comes out and as soon as I saw it, I went to the store and I couldn't believe it. Not only was it what I wanted, it was beyond what I wanted. Turn it upside down and it would still work. It was just the thing I had been looking for for years and years. It was almost my dream device. And despite not really having the money to buy it, I bought it anyway and immediately adored it. I showed it to all of my friends and they thought this was some sort of a silly, niche device, they couldn't believe I spent money on this. And I said, no, no, no, you have to understand this is the future. This is what everyone's going to be doing. This will free us from our computers. And after a while, maybe six months, my friends finally saw all the different things I was doing with it and decided was for them too. So eventually they followed my lead. Everything on it, I read, I played games. I mean, you name it. I did it on this iPad. I used it like a laptop even though it was not prepared to be a laptop way back in 2010. And now it brings us to today. I no longer have that first version iPad. I do have the first version of the iPad Pro that came out because big is amazing. I even had one of those magazine subscription applications that Apple eventually bought and I loved reading magazines on the iPad. This iPad Pro went with me everywhere. And in fact, when I would go to training sites, all the other trainers would have these huge stacks of manuals they would go through page by page. But there I was with my iPad Pro flipping through the pages and walking up and down the aisles so I could help people get through the training manuals. Just was my favorite thing. I eventually did buy a mini and I liked the mini just fine. It's a perfect kind of bedtime companion. I wanna check a radar, I wanna play a quick game. I can do very quick and small things with it. I do love my mini. But I also bought the smallest mini possible and quite frankly, 64 gigabytes just does not do it for me anymore. So my eye started looking towards buying a new iPad. But the question came out. First of all, do I really need an iPad? I have a MacBook, I use it all the time and it goes with me everywhere I go. I travel less than I used to before the pandemic and quite frankly, I have the iPad mini and I maybe don't even really need another iPad. My iPad Pro still chugging along. I use it as a way that I can look at certain data all the time despite the fact it's old and it has a very old processor. It still has an amazing screen and to be my weather station, it does a great job. But now what do I do about a new iPad? I'm being a little bit cost-conscious lately just because I'm trying to save money and did I really want to buy a new iPad in general? I did get a bonus from my work and used most of it to buy gas and food which was really boring and not in the spirit of a gift for your 15 year anniversary. So I started looking around and the question always comes along whenever you're buying Apple devices is now the right time? Are they gonna come up with something new and amazing? Are they going to do something very different? I'm curious about when major changes happen something monumental happens but I never use an iPad for a camera and when people talk about bezels my brain just can't handle it. I don't care about bezels at all. Yeah, I know, I came from the windows world. We don't have bezels in windows. When looking at the prices I saw a few of the iPad errors that were on sale but I really wanted the iPad Pro primarily because it used Face ID which I know is a silly reason why but I don't have fingerprints. I could commit almost any crime and you couldn't tell what I was doing. You're just lucky that I'm not a criminal because you would never find me but Face ID was a big changer. Having the M2 chip means that it's future proof. It's gonna last a long time and so my heart was saying the iPad Pro my budget was saying an iPad Air and when I looked at different prices suddenly at Costco they put the iPad Pro 11 which is exactly the size I want on sale. I ran out, bought it and now that's what I have. A few weeks ago my best friend picked up an iPad Pro 12.9. She walked into Best Buy. She saw the Magic Keyboard. She saw the iPad Pro and she says this is what I want picked up the whole thing she just loves it but then I had my new iPad Pro and I was excited to do things. One of the uses that I had needs probably not much of a need is that I want to build up the social media game that I'm doing for my podcast and one of the things that a lot of productivity personal improvement podcasts do is they create memes or tips sheet and I can't read my own handwriting. I'm not very artistic. My friend and I used to do these cute cartoons though in college and I thought what if with her new iPad Pro and my new iPad Pro and we both have pencil too maybe we could start drawing these cartoons all over again and create our own artwork so we can put on our own social media. This is gonna be a great idea and the last few weeks we've been sitting there with you two and the Procreate app that comes on iPad and just learning how to use the software and we've created some fun images with it so there was my first big use case beyond just games and being able to watch things on planes I wanted to learn how to draw. Now I would be lying if I didn't say that Allison used her strong persuasion to help me buy an iPad. I was a little bit on the border but she pushed me over the edge but she also made the point that I had to get the magic keyboard to go with it or really any keyboard and I replied I don't really type on my iPads but that's because you don't have a great keyboard for it. I had the Folio keyboard for my old iPad Pro and to be honest with you I kept leaving it places just because I never typed on it it was mostly used as a cover for my iPad. As most of you you probably wish that you could go without any sort of cover on your iPad because it just makes it heavier and clunkier and aren't those devices just better when they don't have anything. The old owner of my company used to just make fun of me because I always had the most complicated and somewhat heavy cases for my phone, for my iPad and he tried to tell me that the joy of owning an iPad is just to walk around with it with no case at all. It's supposed to be light and then I thought well he probably has the money to replace it if he were to drop it and shatter it into a million pieces. I really don't. So buy cases for my iPads and in this case I did definitely want to get a case not so sure about the keyboard. My friend had the Magic keyboard which she really likes. It's great because it can sit on her lap. It has that floating appearance to it but it's a screen at the right angle and even on her lap she can type anywhere. She responds to emails she's able to take notes almost like it was a MacBook for her. One of the reasons that she picked an iPad over a MacBook is because it has a touchscreen. She loves a touchscreen. But for me, just really don't do it that often. If I have an email to write I'm fine with the onboard keyboard with my phone or my iPad and it's not really what I do with it. So I started doing some investigation and found a lot of different cases. I thought about just getting the folio cover. I just thought about just getting a light keyboard. I thought about just taking the Bluetooth keyboards I had around the house and bringing along and just use it for those cases where I need it but I still wanted that case. With my research, I found the Logitech Combo Touch. It's brand new, it changed quite a bit and I noticed that many of the complaints that people had with this version of a keyboard case in the past have been fixed in this particular version. What I liked about it in particular is the keyboard detaches. So when I don't need it, I'm just sitting around using it on my couch or I'm drawing with it and I don't want a keyboard I can use the kickstand behind it and use the device without having the extra weight. We'll talk about measurements in just a moment. So from my friend's point of view with the iPad 12.9 and the case together she found that it was heavy, it was hard to carry around and she pulls it out of the Magic Keyboard for iPad all the time when she's just watching TV. So she feels, while she likes her case and that it's very grippy and she feels her device is very safe in it, she also can tell that it's very well made. It also adds a lot to the iPad and she ends up removing it just to have an iPad. She ended up getting just a polio cover so that when she is around the house she has something to give it a little bit of protection. When I bought the Logitech Combo Touch the first thing I saw is that it was woven. It's this kind of woven material on it. I didn't know really what it is but in doing some research they say that it's actually some form of plastic that has been woven together. It's fairly grippy although it can be a little bit slippery at times. I wonder if it's gonna start looking dirty over time because it feels more like a fabric but if it's plastic maybe not. I know that with the iPad Magic Keyboard that can be cleaned and complained with water and it will probably look great for a really long time. Overall the case feels very rugged. It gives a nice rim around the screen of the iPad so that it passes that flower test. If you've ever heard of the flower test it's when you turn an iPhone or an iPad case over with flower on the table and does it pick up any of it. It's because it has that little lip that prevents the screen from getting scratched if there was something on your table, very small that could potentially scratch it. I find that has been the most helpful thing over my years of owning Apple devices. It has a kickstand in the back and I know that kickstand is not everybody's favorite method.  I tried it today and it just flops over and it doesn't really stand upright unless you fiddle with it quite a bit. But if you're sitting at a table, it works just fine. The other thing people talk about is if you're on a plane where the table's very small this might have some trouble because those kickstands come out just a few inches behind it which makes it not as useful on an airplane. But again, I don't foresee myself typing on an airplane so I didn't feel like that was much of a problem. The kickstand goes into two different positions. One that's great for watching TV or typing on the keyboard when it's attached or the other one folds over a lot more and it makes a great writing surface. So if you're taking notes, you're doing some art with the pencil it's at that right angle for you to use your wrist to write something. In past versions of this keyboard people complained that the keyboard itself when you take it off didn't have a place to go. It doesn't really flip over backwards. But what this does is you can turn it around so that the magnets reattach and then it goes back into the bottom of the iPad. So the keys are protected and they don't get all messy. So they heard that piece of advice and now they have a way of protecting your keyboard but keeping it with the whole ensemble all the time. I tested the keys, it has a nice feel to the keys and it also has a trackpad that works really well too. Although again, I'm a touchscreen person just like my friend and I'm also very used to using touchscreens. So I go either way whether I'm using that. Past versions of this particular case had batteries in it and you charge the battery to power the keyboard itself but this actually just runs power directly off of the keyboard and that also gives it its responsiveness but it also doesn't need that spare battery so that you have to keep it charged. There is no pass-through connector like the Magic Keyboard for iPad has which means when you have your keyboard in the case there's a charging socket in there which leaves your USB-C Thunderbolt port for other things if you're adding other types of pieces like a microphone or some other device it's free to do that. In this case, there's no pass-through charging at all. Again, I don't think for me at least that's going to be a problem. One of the nice things about this compared to the Magic Keyboard for iPad is it does have audio and visual controls at the top of the keys which means you can turn up the volume, turn down the volume, turn up the brightness, control the brightness of the lighted keyboard right from the keys themselves. And that makes it nice. The Magic Keyboard for iPad does not have that which is interesting because I saw a lot of people if they had a complaint about this keyboard that was it right there. When it folds up, it has a little lip where the magnetic pencil too can connect to the iPad like it always does but it gives it a little bit of a perfection. It used to have a strap or a little pencil loop in the past. No longer has that which makes it nice for easy removal and putting it back but it also means that it's not quite as protected as it used to be from falling out into your bag if you did shove it in your bag. But I feel that this whole case around my iPad gives it a lot of protection, makes it very safe and I feel that if I shove it in a bag it's not gonna get scratched in any sort of way. I've already scratched my iPad mini by having the folio cover for it and putting it in a bag and somehow the magnet didn't stay to it very well. So let's talk a little bit about some of the statistics that we have for these. The iPad itself weighs one pound 0.04 ounces. It's seven inches tall and 9.74 inches wide and it is 0.23 inches thick. So right there you already have a pound. This makes it 0.6 inches thicker to have the Combo Touch case on it, which isn't too bad. I didn't feel or I don't feel that it's too thick or too large to carry around. And so then the Logitech Combo Touch is 10.31 inches total by 7.67 inches and for a total width of 0.83 inches. It weighs all by itself 1.39 pounds which is more than the iPad itself weighs but if you take the cover off that is 0.65 pounds lighter which means it reduces the weight of the entire device quite a bit. But the dimensions of the Magic Keyboard for iPad is a bit smaller and the weight is 1.1 pounds instead of 1.3 pounds making it a little bit lighter but then there's no opportunity to remove the keyboard to make it even lighter yet. So it's just a matter of choice which one that you like to have. So here you bought a new iPad maybe even went in for the pencil but your wallet is about to get a little bit lighter. Let's compare the prices of the two devices. For the 11 inch iPad Pro the Magic Keyboard for iPad comes in at 2.99 at the Apple Store. Other retailers can sometimes discount it all the way down to 2.29 for the same iPad Pro 11 inch. If you want to get it in the 12.9 it's a little bit more expensive and if you want to buy it for the iPad Air it gets a little cheaper. For the Logitech Combo Tuck it comes in at around 1.69, 1.79 and it retails on their website for 1.99 there are occasional discounts there too. Again if you're going to buy the 12.9 a little bit more expensive and if you're going to buy the iPad Air a little bit cheaper. With the Magic Keyboard for iPad there's two positions it's either 85 degrees or 130 degrees depending on how you want your viewing to look and that's great when you're using it almost like a laptop replacement. But when it comes to drawing on it neither of those two positions work very well. So I think my friend is very happy with the Magic Keyboard for iPad it allows her to take her iPad everywhere she goes and then type on it she loves to write notes and for me I think the Logitech Combo Tuck is great for me too. I feel safe in it I feel I can pack it in a bag and particularly when I go on trips on planes it's going to be safe the pencil is always attached and when I'm just walking around the house the keyboard comes off and I have a nice place to stash that when I'm not using it. My friend is happy I'm happy and we both have iPads that we can use for whatever types of purposes we have. I'm looking forward to doing more with my iPad right now I'm getting it all set up and going through those procreate tutorials on YouTube. Hopefully someday you'll start seeing social media memes coming from me and my friend as we start to promote our podcast. I hope this review helped you in looking at a different type of case for your iPad and other considerations when looking for a case we're both happy and thrilled with our new iPads. Again, this is Jill from the North Woods you can find me on Alison Slack channel if you have any questions or comments and you can also reach to me at my website smallstepspod.com Well, this is absolutely terrific Jill. Now to the audience she's telling the truth I really did push Jill to get a keyboard but I love that she found a different one that makes her so happy. By the way, Jill made one slight verbal typo when talking about the Magic Keyboard for iPad Pro she said that it had two positions 85 degrees and 130 degrees what she meant to say was that it has a range of position from 85 to 130 degrees. Now she's a hundred percent right that nowhere in that viewing angle is it any good for writing with pencil. I always tear my iPad off the Magic Keyboard when I want to use pencil. Thanks for the great review as always Jill and for telling us about the Logitech combo keyboard case. I'd never seen it before and I kind of want to try one of those too. All right, let's have a listen to a prerecorded interview I did at the CSUN Assistive Tech Conference a little bit ago. One of the problems for visually impaired people is being able to tell when the light is green or they're allowed to walk to cross the street. A company called IAS is working on a product called OCO that is supposed to make this easy and I am standing here with Michael Janssen who is from Belgium. We love Belgians of course on the podcast and so he's going to tell us about it. Describe how this works. Yeah, sure. Hey, nice to meet you everyone. I'm Michael indeed one of the founders of a company called IAS. We basically started off two years ago. We have a buying family friend in Belgium and he told us about the challenge of crossing the street in a safe way and that's why we've developed a mobile app. Of course these days only on iPhone but basically what we do is we use a camera of your smartphone and artificial intelligence to analyze the pedestrian traffic lights status. So we convey the walk signal or the don't walk signal through audio and haptic feedback such that they know whenever it's safe to cross. Oh, that is really cool. Now we've just traveled to other countries. Those signs are different everywhere you go. I mean, in Argentina, there were like 11 different things that showed but in the U.S., is it fairly standardized? It's fairly standardized but it's completely different than for example in Belgium or just throughout Europe. And that's why it took us so long to make the AI as good as it is in Europe and translate that in the U.S. So we're- I can imagine. Yeah, it's different everywhere. Yeah, because our service is already live for about now a year ago in Europe and now we're three weeks here in the U.S. So that's pretty exciting. Before we got started, you were explaining that a lot of traffic lights do have like an audio beep telling you you're allowed to walk or don't walk or a clicking sound, but that's not standardized. And you said it's not very well maintained as well. Yeah, there's not a lot to correct. There's not too, a lot of those audible speakers. That's actually the problem or the biggest problem. But of course, if there are there, the maintenance is not maintained well. So they're not always working. So that's a very frustrating thing if you're relying on that service. And of course our service doesn't need to have something installed at a traffic light because we literally look at a sighted person at the traffic light and convey that information back. Very cool. So we're gonna try to do a quick demo here. We've got, he's got a traffic light up above us. It's got a little walking person right now. And do you wanna zoom in here, Steve, on the screen? So he's holding the phone up to look at the traffic light. We have to get farther away because in reality, you're really far away, right? Yeah, indeed, indeed. So describe what we're seeing on screen. Yeah, so the screen lit up green to indicate the walk signal is on. But of course, there's also an audible and a vibration cue. It's a very fast tone to indicate the walk signal. And the don't walk signal is the same pattern but much slower. So a very slow beep to indicate that don't walk signal. Okay, how about that? Run, run, run, hurry. The light's about to change signal. Does it do that too? No, no, yeah, no. But I mean, like if it's got a countdown, what does it tell you? The countdown signal is some sort of a timer, tick tock, tick tock, counting down to just indicate that either you should hurry up and finish your crossing or do not start your crossing if you're just about to enter the crosswalk. So we always are there to convey more information. It's not an replacement of orientation and mobility or a wide gain or a guide talk. We're just another tool on the assistive technology belt, let's say. I think a very important aspect, and that's what a lot of Americans like here, the moment that you start veering off, which is a critical thing as a blind people, the phone will become silent. So if you're rotating to the right or to the left, your phone will become silent and that means that you're veering off into traffic. Well, off of the crosswalk. Off of the crosswalk, indeed. And so what most people do, they'll just put the phone against the chest, the camera looking in the direction that you're walking in.  And that means that people need to reorient themselves to find the traffic light or our system will find the traffic light, of course. And that means that you always need to follow the sound or the vibration to reach the other side of the road. And it was actually Milwaukee two weeks ago that I was a blind user that mentioned it's the first time in my life and she's 2022, that she was able to cross the street in a safe, straight way with our application. Confidence, wow, that is really, really cool. And the fact that the whole screen turns green is somebody listening might think, well, you're blind, what good is it being green? But low vision as well, right? A bright green six inch rectangle, you're gonna, a lot of people would be able to notice that where they don't have the visual acuity to see the sign itself. That's indeed intended for people with low vision to just maximize their wrist feces and just look at their phone rather than a couple of feet at distance to analyze the traffic light itself. This is very cool. So you can download OCO, it's O-K-O in the app store for the iPhone. Nothing for Android though. Nothing for Android at the moment. Of course, Apple has been a pioneer in accessibility and I think a very important aspect, our software runs locally on the phone. So no Wi-Fi, no seller connection is required and Android is still not there yet. And that's why we as a young company focus on iPhone these days. I wondered why you were willing to do a live demo because everybody else is going, oh, I can't do that because the Wi-Fi and cellular in here is good enough but you don't use that so that's proof of it. That's the beauty of it. It's such a scalable thing. It doesn't require the Wi-Fi or seller connection and that's the beauty. What's the cost of using OCO? So we charge it for free to the user. Our vision is if sighted people do not need to pay to look at the traffic light why do blind and visually impaired people. Our mission is to find B2B or B2G partners so working with cities or healthcare partners. Same is true for Belgium, our home country. The app is there reimbursed for all users across the state, let's say. So that's amazing. That's fantastic. Well, this is really cool. I'm gonna download it and take a look and see what it does myself. So it's okay, oh, and thank you very much for helping us out. Thank you very much. I am delighted to introduce the Nocella Castaways to our newest patron of the Podfeat podcast. His name is Keith Kuby. Keith went to podfeat.com slash Patreon and committed his hard-earned dollars to help support the show. His support means a lot to me as does the support of all the people who continue to support the show every month. If you can afford it and you think you get real value out of the show, please be cool like Keith and become a patron. One of the most important applications I use is called Under My Roof from binary formations. Under My Roof helps you keep track of everything to do with your home through a beautiful interface. Under the hood, it's a powerful database but that's hidden from the user so you don't have to worry you're pretty little head about it. Now it does take some time investment to populate Under My Roof but in case of fire, flood, tornadoes, earthquakes or theft you'll be glad you have all of your records in one place. Speaking of insurance, you can keep track of insurance policies and coverage information for your home as well in Under My Roof. I use it to keep track of all of my electronics. I add in warranty serial numbers and photos. You can use it to track collections like say Pokemon cards or Bernstein Bears or Tiki Mugs. Jewelry is another big thing people might like to keep records of in Under My Roof. You can track maintenance tasks as well. Anything that's under your roof, whether it's a house or an apartment can be maintained in Under My Roof. When it comes time to move, Under My Roof helps you by letting you record what you put in each box with photos and when you arrive in your new home you'll be able to find that spaghetti strainer you need on the very first night. I'm betting a significant number of you are thinking well this sounds like way too much work but Under My Roof has such a great interface it makes it easy so it's actually kind of fun. Now as Joe from the Northwood says on her podcast start with small steps. I could recommend by starting out by just just put in new stuff when you buy it into Under My Roof. Once you get the hang of doing it you'll find you wanna go back and start entering things that maybe you've had for a long time. Let's get pricing out of the way. Under My Roof is a very moderately priced subscription of 25 bucks a year. That's USD. For that price you get the app and your synced inventory on your Mac, iPhone and iPad. Now if you'd rather pay month to month you could do that for four bucks a month and when you stop paying the subscription you can still access all of the data in your interview in your inventory. So let me repeat that. You never lose access to your data if you stop paying the subscription. Now you can also even get a free trial with 10 items in it so you can kick the tires yourself and see whether Under My Roof is as easy to use as I claim. Now Under My Roof also supports family sharing which means you can share your inventory and the app subscription with your family members. I used to have to do all of the work to maintain our Under My Roof database but when the fine folks at Binary Formations added family sharing Steve was able to start maintaining his own items. It's so easy to add new items that he picked it up really quickly and he doesn't ever drag his feet about keeping the database up to date. You can also share an inventory with other people who aren't in your family. Now I'm itching to tell you about the fun stuff but I'm betting another big percentage of you are wondering how secure is my data if I put it under my roof seeing that you can share it between users and between devices. Binary Formations is adamant. They do not maintain any intermediate servers. All syncing and sharing is done through iCloud. If you want a bit more security from prying eyes on your devices you can also send an inventory password through the options panel in Under My Roof. So when you search for Under My Roof in one of the app stores you'll notice that it's called Under My Roof Home Inventory Plus. The reason for that is that they used to have a product called Home Inventory and Under My Roof is the grown up version of the same concept. By adding a Home Inventory to the name in the app stores they ensure that people searching find the new applications. Now I was an avid user of the Home Inventory and I've talked about it on the podcast actually nine years ago so it's well past time for me to tell you about Under My Roof. When you first launch Under My Roof you name your inventory and then you create a home. You may have multiple homes. Maybe you have a home in Houston and a home away from home in Austin. Perhaps you manage rental properties or you have a vacation cabin. Under My Roof can handle as many homes as you can afford. The left sidebar of Under My Roof is called the Browse Bar and it allows you to browse your inventory from a bunch of different perspectives. You can browse by location, category, collection and more. I normally browse my inventory by location so I can look at say just what's in my office, just what's in Steve's office, just what's in the family room or maybe just what's in our bedroom. In the bedroom for example, we can have electronics like a home pod, a TV and a receiver but we've also got jewelry that's in the bedroom. Well don't go looking in my bedroom by my jewelry. Anyway, I can see all of those items if I browse by location. Now you can also browse by category so I could say see all of my jewelry or all of my electronics regardless of location in my home. You can also tag items and then browse by those tags. You can browse by all items if worrying about organization is not on the agenda for a given session with Under My Roof. There's a lot more ways to browse your items but let's jump ahead to how to enter items into Under My Roof. I promise to you it was easy so I better hurry up and prove it. There's a lot of different ways to start entering items into Under My Roof so you can pick the way that's easiest for you and under the circumstances that you're in at the time. There's a pretty obvious plus button to create a new item. From there you can enter the details about the item things like what it is, the price, purchase date, serial number, who you bought it from and you can add the location and category. Now if you're using a Mac or an iPad with a keyboard starting with all this text entry works really well. If you've already taken a photo of the item you're gonna import the photo from your photos library directly into the item. Now there is an option to add a photo using the camera from your device but if you're using the Mac or iPad that isn't the most convenient way to take a photo. However, if you're on your iPhone you might wanna start from the other direction. You can take photos directly within the Under My Roof interface so you don't clutter up your photos library with pictures of your stuff. If you're good little typer on that wee tiny iPhone keyboard this is probably a great way to enter new items. You can always add a photo from the iOS version of Under My Roof throw in a quick title on the wee tiny keyboard and then move over to the Mac to enter the rest of the information. There's a third way to create a new item and that's to use the inbox. On the Mac or one of your iOS devices Under My Roof installs a share extension. Recently my good friend Pat Dangler gave me a brother laser printer. I took three photos of it right after I set it up but I didn't have time right then to mess around with adding it to my inventory. I use the share extension from photos to send it to Under My Roof inbox and when I opened Under My Roof on my Mac at a convenient time I had a notification to check the inbox. I selected the three photos from there and I was able to create the new item from those images. I really liked being able to time shift from some of the tasks with the inbox feature. I do want to make one comment about taking photos of your stuff. When you take photos of an item make sure that you're in the photo with the item. I know that sounds kind of funny but when all of our jewelry got stolen many years ago by the now defunct airline TWA our insurance company told us it was very important. He said anyone can supply a photo or a copy of a receipt but that doesn't really prove that they ever had it in their possession. They wanted photos of us actually with the jewelry that got stolen and by the way we got everything paid back because we were able to provide those photos of us with our jewelry. Now I really like the flexibility of Under My Roof in how it lets you use the right tool for the right job at the right time whether you want to enter a photo first whether you want to enter text first whichever way you want to do it or just send something to the inbox to deal with it later. Now once you have a few items added to a location or category or tag you start to get the feel for how easy it is to navigate the interface of Under My Roof. You have the browse bar that I mentioned on the left then there's a column showing all of the items you've added with nice thumbnails so it's easy to see the items. Then on the right you've got a bigger area that shows you the details about the item selected.  It's efficiently laid out to give you the information you need right at your fingertips. In addition to adding photos to items you can add receipts for purchases and warranties and you can add repair information. While I was working on this review I realized I'd never recorded the repair done to my MacBook Pro last year so I hunted the information down in my email and uploaded the PDF to Under My Roof using the inbox feature. Now when entering warranty information be sure to put in the term of the warranty. Under My Roof will automatically calculate the end date of the warranty and your item will reflect when it falls out of warranty status. I know with Apple Gear we can always check online for this kind of information but I really like having it for every item in Under My Roof. Now some items you might want to add by barcode rather than typing in all of the information by hand. For example we have an extensive DVD collection and that's a perfect thing to record as a collection in Under My Roof using barcode scanning. Under My Roof supports scanning of UPC, EAN and ISBN barcode types which when successful really speeds up the process of entering your items. As you would imagine this is a good time to use the iPhone to do the scanning rather than trying to hold the DVDs up to a camera on a Mac. It might work but I like using the iPhone better. I tested using the barcode scanning option to scan in our Tom Cruise movies. In my experiments nine of my Tom Cruise movies popped right in. One of them took four or five tries to get the scan to work and the last three never scanned properly at all. I'm not sure why this is but I've had the exact same experience when scanning movie barcodes into another database app that I use. Now I did find that my success rate went up with diffuse sunlight rather than direct light which could cause reflections. Now upon successful scan under My Roof enters the basic information for the DVD such as the name and description but it didn't pull in information like director, actors and genre or the artwork. I still needed a photo of that. Now I use DVDpedia from Brugge to manage our DVD library because it does pull in much more extensive information about the DVDs but I just want to use that as an example of how you can scan in anything that's got a barcode. Now if you ever given something away and then later on you can't find it in your house because your memory's as bad as mine maybe you float an iPhone down to your nephew and then you go looking for it to use it as a continuity camera and you can't remember where it went. And under My Roof you can set a flag on any item as disposed. Simply right click on the item using a Mac or long press if you're on iOS and select dispose. You'll be given 12 different options for how it was disposed of. Broken, deleted, destroyed, donated, gifted, lost, other, recycled, returned, stole, stolen or trashed. Others in the middle there because it's alphabetical. Anyway, depending on the option you choose you might be queried for more information. For example, if you choose sold it'll ask you how much you got for it. If you choose gifted it will ask you who the lucky recipient was. Once you've disposed of an item it's removed from locations, categories and all the other ways you can look at items in the browse bar. But at the bottom of the browse bar is the option to view disposed of items so they're still available to you when you wanna know to whom you gave that iPhone. If you really wanna get rid of it there's a trash can available to you there or you can right click and choose delete. Maybe you think it's silly to track the stuff you no longer own but we have definitely used this feature when we couldn't find some luggage we swore we used to have. Now items in your database can only be in one category but under my roof supports subcategories. An example of this of how to use this would be to say have an electronics category but also have a subcategory for cameras. The other nice thing about subcategories is you can create them after creating the original categories. An example I just gave I had two parallel categories but I right clicked on the cameras category chose edit and I had the option to make it a subcategory of an existing category. Now in the browse bar under categories electronics has a little chevron inviting me to flip it down to see my camera's subcategory. A new feature in under my roof is the ability to manage maintenance for everything under your roof. Steve and I know that changing the air filters is important for our health but we just don't seem to remember when to do it around Casa Sheridan. At the top left side of, I'm sorry at the top left of the side panel that normally shows the browse bar you'll see a little hamburger menu. When selected, this opens the options panel which is where you can enter maintenance tasks. Think about changing the batteries in the smoke detector, changing the air filters like us or maybe having your solar panels cleaned whatever maintenance you need to do around the house the annual flush of the water heater that's a good one too. You can put in the last date you did it and set up regular reminders for when you need to do it next. But that's not all. If the maintenance requires supplies like our air filters you may have trouble remembering whether you bought extras last time where you might have put those extras and if you didn't buy extras which exact air filters do you need to buy? For this we take a trip back to our friend the browse bar where we can manage supplies for our home. You could scan the bar code on the supplies if you like or enter the information by hand. In my case I entered the part number including the size, how many I have in stock that's important and for location I told myself they're in the garage. I even threw in a couple of photos of the filters so they'd be easier to find the next time we need to go buy them. Now once you have the supplies entered you can connect this supply back to the maintenance task. Let's say you buy a pack of six air filters at Costco but you only need to use two each time. When you complete the maintenance task when reminded your quantity of supplies will go down from six to four. When it goes down to zero you'll be notified so you know to go buy more.  Oh wait, there's more. The most tired I have ever been in my entire life was the last time I moved. There is a reason I've been living in the same exact house for 33 years. When you do have to move under my roof can make it easier. Turns out you can make or buy barcode stickers of your own to put on your moving boxes. You can scan those codes into under my roof and enter what did you put in each box. Heck just take a photo of what's inside each box before you tape it up and you can have that in under my roof as well. When you get to your new home on the other end instead of rummaging through every box looking for things you can scan a barcode and check to see what's in that box using under my roof. Whether you're an organizational master by nature or a detail oriented person you can still imagine that throwing things into a box sticky a sticker on it taking a photo of scanning a barcode would greatly reduce your stress when unpacking your belongings in your new home. In fact maybe you don't even have to be as organized as long as you know what's in what box. Now what's a good database without the ability to generate reports? Back in the browse bar you can choose reports to generate information about disposed items, home and locations, item detail by location and collection, item list by category, item list by location and category, item summary by category and collection and all policies on your home. Now if we take a look at just one of these the item detail by location and collection report we get a nice layout of each item with the detailed information and photos in thumbnail form. In mine I can see a summary level information of say how many Star Trek DVDs I have because I did a collection for those, what room and category they're in and how much they're worth. You might think it's silly but we have 300 DVDs and at roughly $20 a piece in case of a fire that's a $6,000 replacement value. So you wanna think about what kind of collections you have in your home. At the end of the report by categories, collections and locations you can see the quantity of items and the total value of the items. Even though Under My Roof has this pretty exhaustive set of canned reports, if you're a database nerd and you like making reports already you know you're gonna wanna create your own report format as well and of course Under My Roof can do that. All right, believe it or not in over 3,000 words, 3,000 words I have not covered everything that Under My Roof can do. To give you an idea of how extensive and well supported this app is the user manual is 141 pages of detailed explanations and screenshots to guide you through every feature. I am just wild about this user manual. It is fantastic. Most of what I know about how to use Under My Roof I got by reading the manual, reading the very simple instructions. The team that created this app it's a husband and wife team by the way are absolutely fantastic at support of this application and you could see that in the care of the user manual. Now I know tracking items for insurance is right up there with doing your taxes in terms of enjoyment but having a beautifully designed application that is rock solid and not fiddly truly makes it enjoyable. Check out Under My Roof for Mac, iPhone and iPad at binaryformations.com. Well, that's going to wind us up for this week. Did you know you can email me at Allison at podfeed.com anytime you like if you have a question or suggestion just send it on over. You can follow me on Mastodon as I mentioned earlier at podfeed at chaos.social. Remember, everything good starts with podfeed.com. If you want to join in the conversation you can join our Slack community at podfeed.com slash Slack where you can talk to me and all of the other lovely Nosella Castaways, even Bart. You can support the show at podfeed.com slash Patreon like Keith did this week or you can do a one time donation at podfeed.com slash PayPal. And if you want to join in the fun of the live show head on over to podfeed.com slash live on Sunday nights at 5 p.m. Pacific time and join the friendly and enthusiastic Nosella Castaways. Thanks for listening and stay subscribed.


So what niches are perfect for YouTube automation in 2024? Here are 5 hot ideas. First, DIY tutorials. With people keen on learning and creating tutorials on home repairs, craft projects, or


So, welcome everybody to the Biaxcel webinar number 74. Today with us is Giovanni Bussi from Scuola Internationale Superiore di Studi avanzati, also well known as CISA in Trieste, and he will speak about temperature pressure control. In particular, first order stochastic algorithm. And I am Alessandra Villa and I host this webinar together with Otto Andersson and we are from the center of accident for computational biomolecular research. The webinar is being recorded, so do you are aware of that. And after the webinar, if you still have some question, you can join and you can interact with Giovanni using a Biaxcel.eu forum. There you will find the category dedicated to the webinar, to the Biaxcel webinar, and you will find the webinar number 74. That is the one that Giovanni Bussi is giving now. And now something about Giovanni. So Giovanni got his PhD from the University of Moderna in Reggio Emilia, in particular he was working on a bit of a initial computation. After that, he joined a group of Parinello in Zurich, and he started to work on the molecular system and molecular simulation. Then he moved finally in at CISA, and since 2020 he got the position of full professor, and CISA he was starting a group on the simulation of nuclear acid. He got several grant among others, ERC starting grant, an important national Italian national grant, and is one of the developer of the open source package plumes. In addition to this, he's also interested in the development of fundamental algorithm for molecular dynamic simulation, and that is the reason why it's today here to speak about thermostat and barostat. So, now I stop sharing, I give the word to Giovanni, please. Okay, can you hear me I should be sharing now. Can you hear me. Yep. Okay, so thank you Alessandra for the very nice introduction and thank you to both of you for arranging this very interesting and I hope useful series of seminars of webinars. So today I will talk about temperature and pressure control using a first order stochastic algorithms. So let me start with some motivation. So, so this is a ground max community mostly so I imagine most of the people here are working simulating, so the beta biomolecules, even though it might be not one of you. So when you simulate so beta biomolecules, typically you would like to have molecules at very low concentration, so in a very large volume. But you cannot do that because it's too expensive and so what you do is, you simulate a much smaller volume with primary boundary conditions. Right. But when you do so then the size of the system that you are simulating is very small so fluctuation starts to matter. And typically you want to be able to make this a very little system that you're able to simulate communicate with the outer world and to exchange heat, and that's what you do using thermostats or work and that's what you do using Barostats or mechanical work. So, in order to do so, you have to run your simulation in a well defined and controlled the ensemble so a case the case of isolated system where the number of particles is fixed, the volume is fixed and the energy is fixed so there's no interaction with the outer world is the that of the micro canonical or MV ensemble and you can simulate that using the Hamilton equations but if you want to model in some way energy exchange with the rest of the world, you have to add the thermostat. And you end up in the MVT or canonical ensemble and similarly, if you want to model exchange of mechanical work, you have to add the Barostat so that your volume will be allowed to change. And this is usually done in a setting where both energy and volume are allowed to change which is this NPT ensemble. In addition, you might also have a number of particles changing and remember if you have a non homogeneous system clearly you could should specify which type of particles are changing so you could control the chemical potential instead of the number of particles one or more of the species that are in your simulation. And often this is done by combining molecular dynamics with Monte Carlo but this is something kind of more advanced and more complicated to do. So today I will focus on basically these two cases which is the MVT or isothermal ensemble and the MPT which is the isothermal isobaric ensembles. So this is my agenda for today I will have two sections. First I will discuss thermostats and we'll give some introduction and then focus on one specific alternate which is stochastic velocity rescaling. And then we discuss Barostats and again we give you some introduction on the topic and then we discuss the stochastic set rescaling Barostat both in its isotropic and an isotropic version and I'm happy to take questions also in the middle of the presentation. I don't think it makes sense so. Or you can just wait to the end as you prefer so. So when you simulate a system which is isolated. You typically solve the amateur equations and you typically use like integrators like the frog or velocity for the. The idea here is that if the time step, the iteration time step is chosen small enough you will sample exactly from the MV or micro canonical ensemble which has this expression for the probability to extract a given set of configurations and velocities. A thermostat is basically a modification of these equations of motion so you don't solve it anymore than it's an equation but you add something to the evolution of positions and or velocities. In order to sample from this ensemble instead. You see where basically the probabilities is equal to an exponential of minus the energy of the configuration divided by KBT. I said that you could modify the equation of motion for the positions, this is possible actually this is done with so called configurational thermostats. So in configurational thermostat you modify the velocity in some way that sorry the rate at which the positions are changed. I wanted to mention this because this is a special case that is often ignored. So these algorithms are not very popular, but still I think it's worth to know that it's possible to do so. On the other hand, most of the algorithms used to control temperature are acting on the directly on the evolution of the velocity so they are kinetic thermostats. I would say all the other thermostat except for this very special selection. And again, I think this is a very interesting topic, but today I will focus on kinetic thermostats. Then you have another distinction that you should make, which is between local and global thermostats. Examples of local thermostats are listed here like the Langevin equation, Anderson, Massive, Nosei, Hoover, dissipative particle dynamics. In all these cases, you add a force to each particle, which is independent to some extent to the force that you add the other particles. Every particle is thermalized independently of the other ones. On the other hand, in global thermostats you basically control all the particles simultaneously. So one way of seeing global thermostat is to say that you have a friction, a single friction you see it's not depending on the index I, which acts the same friction on every atom of your system and this friction could be time dependent. Another way of seeing these algorithms is that basically at every step you scale all the velocities by the same multiplicative factor. So what's the important difference between these two types of thermostats? So the global thermostats, so local thermostats, thermalized also in absence of collision. So imagine that you have a simulation box like this with two subset of particles, some of them are hot in the sense that they're moving very quickly. Some of them are moving more slowly. And a global thermostat would sense the total kinetic energy that perhaps is fine. A local thermostat would find that these particles are too slow and will thermalize them separately from these particles. So if you have a system that could be decomposed and some system with very poor interactions, typically a local thermostat is a much more robust choice. Clearly it could be more difficult than this where you have some degrees of freedom that are not very well coupled with other degrees of freedom. So instead with global thermostat, you will have to assume that collisions between particles are sufficient to basically lead to equipartition. However, there are also other differences. So, importantly, the effect on dynamics of global thermostat is much smaller than the effect on dynamics of local thermostats. And this can be seen in this figure, or some specific choice of global and local thermostat but you see as a function of the control parameter tau of the thermostat. You see the diffusion constant. It's basically independent of the choice of the parameter, the diffusion coefficient for global thermostat whereas for a local thermostat. If you choose a too high friction in this case, you end up in a very low diffusion constant. So, dynamics is severely affected by local thermostats. And in addition, and this is more qualitative and probably system dependent statement, it has been seen that global thermostat are much more efficient to equilibrate condensate the phases. So, unless you are in a system where you have many particles which are really the coupled. So if everyone is interacting with everyone in some way, usually global thermostats are much more efficient. So, one way to understand these smaller impact on dynamic is by looking at this graph, you can imagine your momentum as a high dimensional vector if you have 100 particles it would be 300 dimensional vector. So, let's say that at some point, the value of the momentum vector lies here, applying a local thermostat would bring the momentum vector anywhere could move it to anywhere else. Whereas for a global thermostat you would only move it in this direction so the change in the momentum will be proportional to the momentum itself. So, imagine the amount actually in a scaling operation on the momentum vector and remember it's a scaling done in very high dimensionality so imagine this in dimensionality 300. So you move in one direction, and you do not move in 299 directions so you basically remove all the change in, in the velocities that lead to transfer of energy between particles, and all the keep the change in energy to these two global kinetic energy. That's what you do with the global thermostat. So how, how are they implemented the so basically all global thermostats can be implemented in this way you just evolve on the two equations without thermostat you compute the kinetic energy. You propagate the kinetic energy and that's what's what's not in a different way for depending on the term of stuff you are using and then you rescale the momentum with a factor that depends on the new kinetic energy and the old kinetic energy. You can achieve a new value of the kinetic energy. Then here you find a table with some example. So, velocity rescaling Berenson, they are deterministic schemes. They are here in red because they are well known for reporting an ensemble, an ensemble which is not canonical so you don't basically obtain the correct fluctuations using the schemes. Return the correct fluctuations some of them are stochastic some of them are deterministic and I will particularly focus on this one, which is stochastic and the first order. So what do I mean with first order so let's have a look at how the kinetic energy is propagated in this stochastic velocity rescaling scheme. This is the current that you expect in the kinetic energy given by the thermostat. So you see there is a restoring term that brings the kinetic energy towards its target value this KB K bar will be just a three half number of atoms KBT typically. This is actually this term is identical to the one that you have in the Berenson thermostat which is also first order but is missing this stochastic term. This is the first order which is this tau t that controls how quickly the thermostat will force your system to relax towards the correct average energy. But importantly you have an additional term here which is stochastic, and that is able to enforce the right fluctuations and here you just have to plug in the number of degrees of freedom of the system, and everything else is defined so this equation is nice because this part is equivalent to the well known and widely used Berenson thermostat and this part reconciles the correct fluctuations. Another nice thing is that this equation even if it looks a bit complicated can be solved analytically, which means that you can exactly draw a new random kinetic energy corresponding to having propagated this equation so you don't need to do use complicated thermostat as a stepping algorithm to integrate the thermostat itself. So, why is it in interesting and useful to have a first order thermostat, which gives a correct fluctuation so the traditional pipeline, the suggested protocol for many years has been to do like an equation using Berenson thermostat, which doesn't give correct fluctuations but on the other hand equilibrates very well. And then you do production using something like Nose Hoover thermostat perhaps something which typically second order and give you the correct fluctuation having a first order algorithm that can be used both for production and production it's very convenient, it makes the, this little detail that nobody wants to care about which is a choice of the thermostat a little easier to choose. So how can we see this thermostat in action and how does it compare with other possible choices so this comes from quite old paper, this is where we introduced the scheme. So here's a calculation I've done with the poly that is for a Leonard Jones solid and for a Leonard Jones liquid and here what I report is as a function of the tuning parameter this towel. I report the value of the fluctuation of the kinetic energy or of the potential energy for different schemes. So you see basically that with the Berenson scheme, the fluctuations are depending on the choice of towel. Depending on how you choose the towel parameter you will get a different result that's not good and it's well known actually the fluctuations are too small in both cases. The Nose Hoover scheme is supposed to give correct fluctuations. It does so in a wide range of values of towel, for instance you see here it does reasonably well when towel is very small, however, it has troubles. And I guess this is actually due to the way this has been technically implemented in the body, but the fact is that the questions of motion for the Nose Hoover cannot be integrated exactly so you have to find out how to integrate them and for some type of towel. You have to be very careful in not introducing integration errors for a solid there's something interesting that happens even for very large towel. You have artifacts with the Nose Hoover thermostat and this is something which is also widely known that the Nose Hoover thermostat is not working properly for a harmonica oscillator and so solid switch can be to some extent described as harmonic in some regime of the choice of the parameters give problematic results. This is a similar test done for ice and water where you see what system is maybe a bit more relevant and you see a very similar behavior and also here you see that for a large value of towel basically with the Nose Hoover thermostat you could end up in incorrect values of the fluctuations. We can also look for dynamics I mentioned these already quickly in in design eyes we took this trajectory for ice and for water so for eyes we computed the vibrational density of states just as the free transform of the velocity autocorrelation function. You see that if you run without a thermostat that's a solid line or with this stochastic velocity rescuing with very different settings, you basically get the same, the same properties. And the same is true for the diffusion coefficient. Basically you get the values which are very close to those that you obtain using a simulation without a thermostat. And this is not a specific property of stochastic velocity rescuing the fact that the dynamic is largely unaffected is a property of all global thermostats. As I explained it's because they are designed to minimize the impact on the trajectory. And actually the reason why you see this is that there are many atoms so if you imagine to apply a global thermostat to a system with five atoms you will see a lot of impact on them. And the other important thing is that we are monitoring properties that are very different from what the thermostat is acting on the thermostat is acting directly on the kinetic energy. If you look at the dynamics of the kinetic energy it will be very different with the thermostat or without. But if you look at local properties, they will typically be not much affected by global thermostats in general. Okay, a common question, at least in the past has been what about flying ice cube so this is an effect that was detected many years ago it's an artifact that comes out with velocity rescaling, and with the with Berenson. And basically you can visualize it as your system completely freezing and where all the energy goes into the center of mass. But in a more subtle way you can see that basically the equipartition is not achieved so different degrees of freedom have different amount of energy. So in this work, you can see a comparison of different schemes, and you can see that basically in the Langevin chain, also stochastic velocity rescaling, they all provide correct equipartition, and the problem is so it's not related to the scaling itself, but to the way the scaling is done so the problem only appears for balance and for simple velocity rescaling. Another, I think, interesting question is who cares about the fluctuation so of course if you are computing the fluctuation is important but let's say we are computing something else should we be careful about the fluctuations. There's another paper, paper by the group of Gader Hummer 2008. So yeah they only compared no thermostat Berenson thermostat and Langevin thermostat at different fluctuations in the potential energy that's known and expected. But what was kind of unexpected is that if you apply this thermostat in a tier and dissimulation you will get incorrect results in terms of looking at the fraction of folded protein that you have in your system as a function of the temperature. So this I think is very interesting because it means that there is indirect effect only on properties that you might believe to be sort of independent of these fluctuations. And actually even if this paper was published like just one year after our paper. And the reason why I started to work on this topic is exactly this I was playing with rapid exchange I found out that the results with velocity rescaling were wrong. And, and Micaela, my supervisor told me, let's try to fix the thermostat because I was using real poly and there was this velocity rescaling I fix the thermostat and the artifacts went away and then we realize okay this there is a very nice way of fixing velocity rescaling thermostat to make it produce correct results. So, actually, all these problems are related to the violation of the tail balance. We can quantify how much our trajectory is violating the tail balance so this is the flow chart that we have so we first evolve our trajectory using Hamilton equations. So if this is done with a small enough time step energy will change very little. This energy change is actually violating the balance. So it is incorrect. It should be zero. It's not we have to accept the fine time step. On the other hand, when we propagate the kinetic energy, if we can solve our differential equation exactly and we can for our thermostat, then the energy will change a lot because possibly you will have a large scaling factor. But this will not violate the tail balance. So there's something that is explained in detail in the paper, such that you can basically some all the energy increments that are coming out from the evolution of Hamilton equations or, in other words, subtract all the energy changes given by the thermostat and obtain some effective energy that is like energy of the system plus energy of the bath. That allows you to monitor how much are violating the tail balance. Let me show this in practice again this is Leonard Jones liquid. The plots are just shifted for clarity. This is energy conservation in a NVE simulation, no thermostat. And this is effective energy conservation using the thermostat and you see it behaves very, very similarly you have no systematic drift or very little drift maybe as small fluctuations. If you go to a very large and definitely incorrect for the system time step you will see that energy will drift up so you see at the beginning of this plot, the two simulations behave similarly then of course, when the energy becomes too large there are two simulations and so the system does something strange and at some point it explodes whereas with a with a thermostat we just have a constant drift that you can measure I can you can use to assess your integration errors. So that's why it is effective, you can define a sort of effective energy that includes the energy of the thermal bath. So these formulas can be used to define the effective energy also for lunch event thermostat that you can do it for no say Hoover if you do so you end up in what's traditionally been used as conserved energy for the most of the thermostat. And for balancing you cannot do it because the algorithm per se is not time reversible. This has great has been published in 2007 and now it's, it's widely available in many of the codes, the names are different so you have this CS VR in Lambson CP to K, sometimes it's called busier busier or your Parinello, or BDP, it's available in Gromax and this is T coupling equal to via scale where you can also use it. You can use the coupling separate groups independently and if you want to implement it yourself. There's some function here that could be useful. And then to summarize this part, I tried to explain the difference between the local and global thermostats why global thermostats are interesting. I introduced stochastic velocity rescaling which is the global first order so it operates fast and in a predictable way. It gives correct fluctuations allows you to monitor energy conservation and it's easy to you tune and to implement and then if there are questions on this part maybe I'm happy to take them now. So if someone has any question just put in the Q&A I have a question and we will unmute you so you can just at this moment ask question on the thermostat, please. We just give a couple of minutes maybe people has to think about okay. So we have a question from can I will unmute him. Yes, please. I permit can you can speak if you want. No. Okay, so I will read the I will read the question. Stochastic thermostat relative to a strictly deterministic one generate more entropy in a fluid or in a gas of space. By using the system toward more fluctuation. I mean, not in absolute term, but only by proportionality to the system and tell me as well. Yeah, so I would say for a liquid I would say no. It should not depend on the fact that the thermostat is deterministic or stochastic for a gas of system, the real answer is, I don't know so basically I am very suspicious that any global thermostat could work very poorly in a gas of system. Okay, thank you. So now we have William. I allowed you to speak William if you want you can speak. This is about MPT simulation so maybe it's later I don't know. Yeah. Sorry, I arrived a little bit late and I missed the first part, but I have a question about the settings to use and with a low pressure simulation we've been fighting with this for some time and we don't know. We haven't had anything to work even for NPT. We really like to do thermodynamic integration but even NPT doesn't give the correct densities. Could we take this, sorry William, could you we take it after the barostat part. Of course, of course. Yeah, so I will unmute you later. Thank you. Okay. So now we have. I just unmute you. Maybe I can read it. You can speak it now. You can speak if you want. No, you can read it. Yeah, I will. Is the drift only because of high delta T. Yes, in the sense that as delta T tends to zero the drift will disappear. So that's a guaranteed unless there is a bug in your implementation. This is also very useful at test. If there is one further someone asking if we can have the get up link, and maybe they can put in the chat so everybody can see it. Yeah, actually I will share the PDF afterwards. It's a question. I mean, split it and then please solve it just give me a quest moment that I will try to unmute Eric. So, yes, it's chance to, to, to speak. Hi, can you hear me. Yeah, please. Yeah, so thank you for the talk and thank you for the thermostat we we've used this a lot in our work. So my question is, when working with everything here is kind of been about solvated stuff and explicit solve it. How about global rescaling for implicit solvents is that still recommended or do you need those local thermostats to try to capture some of the solvent effects when doing production runs in implicit solvents. That's a very good point in that case, typically people would use like the German dynamics, it's not used as a thermostat but use like to model collision with water as you said so if you want to capture correct dynamics definitely you need to do so. But if you think about it you should do you should do so in a smart way like I don't know maybe surface atom should feel different collisions than the inner atoms in your large protein. It's tricky to reproduce this property, then maybe another related point is for a system which is not solvated who the global thermostat to be efficient. I don't know. I have no really no direct experience so the best thing is to try, try and check there are several papers recently trying to check also equilibration of individual degrees of freedom with the global term stuff. It's possible that you are in corner cases where some degrees of freedom will not be properly equilibrated with a global thermostat. Thank you. Thank you Giovanni, and I will suggest that that we go on we have Louise that has a way to there is another question on the thermostat. Yeah, if you. Okay, if you. Could you repeat what you say using thermostat for a gas system phase. We have no experience with simulation of gas phase systems and I would say that global thermostats are probably not very, not a good idea in this case. Okay, thank you very much Giovanni please. Now we go to the bar stuff. Okay, let's go to bar stuff now. So, here we start with our equations with thermostats. But now we also want to allow exchange of work with the outer world. So to do so, we need to add the volume as a dynamic variable and the distribution that we will sample from we look like this is the isobaric distribution. And then you will have to add some rules to propagate the volume and in addition to modify the rules that you use to propagate positions and velocities, including bar stuff. Depending terms here. So, what does the what is what's the bar stuff expected to do on the coordinates so clearly the bar stuff has to change the volume it could do nothing to the coordinates but this could be very ineffective why because particles that are close to the boundary would feel a very large distance so distances which are across boundaries of your box with boundary conditions would feel very large change when you scale when you change the volume and other distances would be not affected so the most conventional the most common thing is to basically scale all the coordinates and with the same factor, which is basically the cubic root of the change in the volume, then should you do something to velocities as well. This is kind of optional. And I would say in most cases velocity are scaled with an inverse factor but this is not strictly required and we'll see a bit more details. So, actually, and this detail is related to what you want to define as the internal pressure of the system so imagine when you operate this scaling. When you do this scaling operation, the energy of the system changes and the definition of the internal pressure is minus the derivative of the energy change with respect to the volume. And what you do when you change the volume affects what you're going to obtain as a definition for the internal pressure. For instance, if you scale coordinates and then velocities with an inverse factor as I said, and that's what's done in has been done originally in the Anderson, but also in most other arguments is like this. Basically your definition of the internal pressure will look like this. So if you instead, instead only scale the coordinates and this is something not very common. I've seen this in a paper only. Or this is what is done usually in Monte Carlo barostats. You, instead of using the kinetic energy for this contribution for the ideal gas contribution, you use its average value it's a subtle detail but remember we are trying to reproduce corrective fluctuation so these subtle details are very important. You have only choice you have other choices you could decide for instance to take the derivative of the energy, just scaling the center of your molecules, but without changing the internal distances in your molecule this is convenient for instance if you have system with the, with the internal constraints and I think this is if I remember correctly this is what's implemented by default in the amber code, and in that case, you should include only the kinetic energy of the center of mass of your molecules or the number of molecules only in this entropic factor and also the, the virial will be term will be computed differently. How do you implement then barostats in practice so you avoid your ametone equations you apply a thermostat and then you have to compute the internal pressure and use it to propagate the volume. And then once you decide what's the value of the new volume you should scale the positions optionally as we said scale the velocities. And again, you have many options this is the list of the most popular ones I already mentioned you can use Monte Carlo to propagate the volume. You have the balance and scheme which is again not producing correct fluctuation but it's very efficient because it's a first order, so it relax directly to the point. And then you have several other choices among which the other one which is first order is stochastic service scaling and now I will go into the details of this. So this is the equation that you will use to propagate your volume. So it looks very similar to what you have in the better and send barostat is a restoring term which depends on the difference between the external pressure which is a control parameter you set it in the input file and the internal pressure which is computed based on coordinates and positive velocities.  But there's also another term here which is them as where you should plug the estimate of the isothermal compressibility of the system. And that which basically depends on how the volume changes. When you change the pressure. So you typically don't know it priori, but you could estimate it. So and you see that in this equation you only have beta T divided by tau P and also here beta T divided by tau P. So basically only the ratio matter it's a single parameter but the typical way of choosing it is to fix beta T with some estimate and then choose tau P depending on how quickly you want your system to relax. And the very important thing to notice is that whereas the question for the term of stuff could be integrated analytically. This one cannot be integrated analytically because P in depends on the volume in a very non trivial way you change a bit the volume, the energy changes because you have particles getting a different distance you cannot predict this in any way. So, this equation cannot be integrated exactly. This is an important distinction. Still, you can implement it and here I will show you some tests that these were done much more recently. 2020 with Gromax. This is also a diesel and liquid water, 3000 molecules more or less. There you see with Parinello Raman, which is supposed to give the correct fluctuations stochastic service scaling and here you have the average value of the volume as a function of the control parameter tau P, and then you have the fluctuation volume of the function of the control parameter tau P. You basically see that the better and send battles that gives you proper average but underestimates fluctuations stochastic velocity rescuing gives correct fluctuation on a wide range, Parinello Raman here it's failing at very small but again I suspect this could depend on also on the way it's the details of the implementation of the integration of this. So, there is one important comment about this beta t the estimate of the isothermal compressibility you can actually compute this isothermal compressibility by running a short simulation in the MPT ensemble and looking at the fluctuations of the volume but you don't know these in advance. So, this is the case of Landau Jones we could estimate it well it's around 0.3 in its unit less. And then if you look at the autocorrelation function of the volume for different choices of tau P, it decays basically as an exponential with the proper time scale tau P. So, this is actually at the large tau P the case slowly at the small tau P the case more quickly. Now what happens with water this is interesting because everyone I guess everyone using Gromax finds this comment saying that the, the isothermal compressibility of water is 4.5 times 10 to the minus five bar to the minus one and use that in the input file. That's actually the compressibility of real water not of tip 3p the the real the compressibility of tip 3p is 6.3 it's larger. So, this is the isothermal compressibility and as a result of that if you run a simulation with the Barrington Barostat or with the stochastic and cell rescaling Barostat, you will find that the volume will relax at the different speed actually you can make a change of time scales like this it's roughly 50% slower the decaying and after you make this change of time scale and overlap the autocorrelation function with the exponential you see very good agreement. You see, so basically if you make a mistake in estimating the compressibility of the system in advance, you will basically make a mistake in how you predict the relaxation of the volume will be. Another interesting thing that you can notice here is that if you make tau P very small, basically the volume will not have time to relax as quickly as the exponential would predict. This is just the dynamics of the volume but you have to imagine that when you change the volume particles have to rearrange if you do it too quickly particles will not have the time to rearrange and the volume will not be able to relax so quickly. What about the integration of the equations of motion, this is more, this is complicated, exactly because there's not an exact way to integrate the equation of motion for V. So, in this work we tested multiple different implementation in particular all of them are tested on this educational code that you can find this link. And here you can see again average value of the volume for difference value of tau P and for different integrators. And all these integrators will fail at some point if tau P is chosen to small. And these are the fluctuations and again you see they are compatible between each other except that they will all fail if tau P is chosen to small. And this is the energy, this effective energy. If you remember that it to before you can quantify the tail balance violation. And this is the drift per step as a function of tau P, you see that the smaller tau P, the larger this drift. Notice that the curve here is missing for the other integrated the other integrated is the one that is easy to implement is actually the only one that we managed to implement in Gromax, but formally is not reversible so formally, you should define an effective energy. On the other hand, the properties of the system like average fluctuations are compatible between these integrators so we thought, okay, it's fine it's, it would be difficult to implement these integrators properly within Gromax so we will only implement the So similarly to the case of the thermostat one could ask so. Okay, obviously if I'm interested in volume fluctuations, yes, they should be computed properly but let's say that I'm interested in computing the free energy difference. So there's this is interesting paper this is a very extensive benchmark. From a series of papers is a sample six. Where they did comparison of free energy calculations using chemical methods and in particular they compare results obtained with Gromax using the Berenson Barostatt and open MM using Monte Carlo Barostatt and they've seen kind of significant difference around 2.5 kg per mole. So, we try to reproduce this using Gromax, and we actually have seen no basically no difference between Berenson stochastic server scaling and Parinalorama no difference in the free energies. No difference in volume fluctuations but no difference in free energy so we were not able to reproduce the discrepancy so I suspect that the difference in the report could be due to some other differences between open MM and Gromax and not to the Barostatt. So my take home message for this is that if you compute free energies with Berenson or even with MVT possibly they would be correct or at least I didn't find any compelling example to show you that you need to use the proper Barostatt to compute free energies. Of course the answer might be system dependent so you have to be careful of course. And again as a side story, it was actually when this preprint came out that was in 2019 that I thought, okay, if really there is this problem with the Berenson Barostatt we should find a way to fix it and actually I had like in my drawer since five years the equations for the Barostatt so that's how the old thing restarted in 2019. So this Barostatt can also be implemented in a semi isotropic formulation with this in the first paper, here basically you can separately control the length, the height of the box and the area of the base of the box. So this can be very useful especially to simulate membranes or interfaces in general. And in particular you can also control the surface tension so you can sample from the so called MP gamma T ensemble. We did some tests to make sure things are kind of reasonable we obtain fluctuations which are compatible with the Parinello Raman implementation and, and as a negative control we have that Berenson predicts a significant number of fluctuations so we were happy, but also I'm not really an expert of these types of systems so I would be happy to receive feedback some people that tried these on other interfaces. You can make your life even more complicated if you want to study periodic solids like crystals, because here you would need to take into account the full bulge box shape so you would have nine degrees of freedom to change not just one not just the three vectors that generates the periodic lattice. So, the pioneering work in this field was a work indeed by Parinello Raman, where they propose the way to simulate these cell shape fluctuations at the proper temperature. There are other algorithms in the literature actually Gromax only implements Parinello Raman. So, and so we at some point we said okay can we generalize our equations to the fully flexible anisotropic case, and the answer is yes.  And again you will need the proper noise to be added in order to get the right fluctuations. So, here we run some comparison. This was done using Gromax, as I said Gromax only implements Parinello Raman for the fully anisotropic case. And here you see that so your trajectories are shifted for clarity, but so the averages are actually equal to each other but you see that fluctuations in the Parinello Raman are really equilibrating very slowly. And I don't know if this is due to the Parinello Raman equations or to the way they are implemented Gromax I really have no idea. In the anisotropic case we were able to compare with also with the MTTK which is Martina to be a Stackelman Klein Barostat, which is available only in the anisotropic case, which gives the results that is similar to our stochastic cell rescaling approach. So, here we have auto correlation functions for different value of tau, and also comparing results obtained with Gromax and lamps. So, the message here is that basically the stochastic cell rescaling here as always like this nice exponential like decaying. The stochastic cell is really just relaxing an exponential way, whereas other algarits will have fluctuations that could that where they could be dumping a different timescale and they could also have a different period, depending on how you set up. apply an external stress. So this is an example with gold, where we applied an external stress to see the formation in the unit cell until the system at some point breaks and you see a slip here. And then we were able to test these different implementation, different bar stats and also static calculations to body data we were obtaining correct results. So what about availability? So for the isotropic and semi isotropic versions, they are basically available in Gromax 2021 app. So this is just the keywords, zero scale. For the anisotropic version, we did this work using a custom modified version of Groma 2021. And so we distribute a patch if you want to use it. And we have now ongoing the review of a merge request on the master branch. So this implementation for the fully anisotropic case could appear in a later Gromax version. Then to summarize this second part, I introduced to you bar stat and in particular stochastic service scaling. It's a first order. It gives right fluctuations. It has one parameter actually apparently two, but you've seen that only the ratio matters. You can define effective energy conservation, even though these require to implement some non-trivial integrator and can be generalized to crystalline solids. And finally, let me thank my collaborators for this work. This has been work done across decades. So the work on thermostats was done when I was still a postdoc in a group of Michele Parinello. And I also want to acknowledge David D'Andio who was helping me a lot, like teaching me how to simulate water. The work on stochastic service scaling was done by a postdoc in my group, a former postdoc of my group, Mattia Bernetti. Whereas the anisotropic version was developed by a master student that was visiting my group in Torre del Tatto in collaboration with the Paul Wright theory from El Carten. And then thank you all for your attention. Thank you very much, Giovanni. It was very nice and clear presentation. Now we go to William that he had the question. So I will unmute William. So he can ask his question. Yeah, please, William, you are allowed. And sorry, in the meantime, I will ask everybody to write if you have a question on the Q&A. Okay, I just unmuted myself. Can you hear me now? Yes. Good. Yes, actually, I think someone almost asked the same question earlier on. It's really, we're trying to do simulations in the gas phase. We want to do NPT and we also want to calculate chemical potentials basically by thermodynamic integration. And nothing seems to work. We, when we know the right answer, this is very low pressures, say 100 Pascals or something like that. Any suggestions? So my suggestion will be that if you are in the gas phase, so for the, but I'm really guessing. So they give you the grain of salt. What I would do is if you want to compute thermodynamic quantities like chemical potential, I would suggest to use Langevin thermostat and to use the steel, this stochastic cell rescaling thermostat which should be stable and should work well even if you have a gas phase system. Because in the end the volume is just one variable. Instead for your particles, you cannot assume that they will be coupled enough for a global thermostat to work. That's what I would guess. I'm sorry. So you can see the Langevin thermostat and what barostat? I would use, I would try this CRSK barostat. What about a Monte Carlo barostat? We thought about that. Yeah, that should give a very similar result. And would be equally good option, I would say. The main difference is the way you tune parameters. For Monte Carlo barostat you typically set the step size for this CRSK, you typically set a relaxation time scale. But I would say I would bet they would give very similar results. And they would have very similar efficiency, very similar properties. Okay, thank you very much. Thank you. Now we have another question from Khan that I could not unmute before. So you can read the question loudly, Giovanni. Yeah, should I read the question? Yeah, so could the barostat cell rescaling steer the system from the Maxwell-Boltzmann distribution perhaps by creating the case which radically violate the Boltzmann distribution at set temperature? I don't think so. So all these moves are done at equilibrium. So provided that the tau P is not too small, in which case you basically will fail in the integration, I don't expect that the barostat will induce violation of the Boltzmann distribution. Okay, thank you very much. Please, if anybody else has a question, please type in a Q and A. Okay, I don't see question appearing. So I will just... So we just wait a moment if someone has another question. No, so I want just to copy. So if you have other question that they're popping up, you can always ask to Giovanni via the webinar link on the forum. So then now I will post it. I will post. So you can see here you can go further to ask more questions to Giovanni. I put there all the questions that you have asked so Giovanni could also answer again in this written form. And I thank you everybody for the attendance and I close this webinar section now and we will go back in spring. So the BioXL webinar for the winter are going on holiday and we will be back around February. Looking forward to see all of you again. Thank you very much for joining. Bye-bye. Bye-bye.