Lima Dynamics

Initial product release It is so exciting to finally write this post. As of today, LIMA is available as a distributed package for Arch and Ubuntu. The packages are available on our shiny new website: www.lima-dynamics.com under downloads. Our proudest feature is a MembraneBuilder for all sizes of membranes - the first of it's kind to be completely free to use. We support the StockholmLipids by default, aswell as any user supplied lipid structure. We invite anyone to try this new feature and share feedback. Should there be any errors, please send an email to support@lima-dynamics.com and we'll try to patch it the same day. Thanks for reading /Daniel

#Devlog 8: Steady progress towards large membrane setups It is not always easy finding content for these devlogs, as the majority of work being done on LIMA is not particularly flashy - but this week is different. We've been working on an algorithm to quickly setup membranes in more complex shapes. I found this visually quite appealing and decided to make a full video explaining roughly how it works. This is only a prototype showcasing the algorithm, in an upcoming update we will use this to make a lipid vesicle. Stay tuned for that! /Daniel https://lnkd.in/dr-h2NrY

#Devlog 7: A new mission: Molecular Dynamics for AI-based drug design Running at full speed on a consumer card, LIMA can generate around 6.6 GB/s of data, or 1 PetaByte every 2 days. This data, in essence, describes how various molecules interact with eachother at a resolution of 0.000 000 000 000 000 010 metres! Such a massive amount of data, can be difficult to utilize effectively. The world however is currently experiencing massive changes at the dawn of generative AI, and drug design will be the next major achievement. Generative models for drug design navigate a configurational space vastly larger than their counterparts in text and image generation, necessitating massive volumes of highly specific training data. And that is exactly what LIMA will strive to provide it's users; a "plugin" that researchers use to stream data of whatever molecule they want directly into their training pipeline. Latest work: The video below shows a large molecule (Proteasome) being loaded from files on a harddisk, onto a GPU to run in less than 5 seconds. While this latency time is already down from 21 seconds, we aim for less than 500 ms to optimize our users workflow. Stay tuned for more updates /Daniel

<edit> Update: Thank you so much to everyone who showed interest in joining LIMA. We have received an overwhelming response and are currently reviewing. At this time, we can not accept further applications. </edit> 🔶 Looking for a computational physicist/chemist🔶 LIMA is implementing Electrostatic Potentials. This is quite a complex task, and.. we might need some help. We are now looking for an in-house field-expert, who: Wants to aid in developing software for Molecular Modeling with superior performance, and simpler user interfaces. Has experience with Molecular Dynamics simulations and GROMACS. Is ready to dive into the equations that allows MD simulations to take place. Coding skills is not necessary. Wants to contribute in the early stages of the startup, as we work towards securing the first round of funding. You can read more about LIMA on our page: www.lima-dynamics.com If this sounds interesting to you, then please reach out to me in a DM, or send an email here: info@lima-dynamics.com I'm excited to get in touch with you /Daniel

#Devlog 6: Membrane builder and support for Ubuntu Imagine a time when access to tailormade lipid membranes required you to apply for a license, wait a couple days for a reply and finally cough up the money it costs to use the software. That might be pretty easy to imagine, because that time was yesterday. However, today LIMA has opened access to an alpha version of our own membranebuilder feature*. A feature that can create a membrane up to 20 nm^2. We invite you to dive into the engine room and see how the feature works, by watching the video below. If this is a useful feature for you, but you haven't downloaded LIMA yet since you don't run Arch, then you're in double luck. As of today LIMA MD is supported for Ubuntu 23.10. As always, simply clone the GitHub repo (https://lnkd.in/ebTBPyBS) and follow the instructions from the README.md and install.sh. To generate a membrane, all you need to do is run 2 commands in your terminal: First generate a parameter file: 𝐥𝐢𝐦𝐚 𝐦𝐚𝐤𝐞𝐬𝐢𝐦𝐩𝐚𝐫𝐚𝐦𝐬 Then modify the boxsize in the sim_params.txt file You can now specify any combination of the following 6 lipids (POPC, POPE, DDPC, DMPC, cholesterol, DOPC), and ensure the percentages add up to 100. Example: 𝐥𝐢𝐦𝐚 𝐛𝐮𝐢𝐥𝐝𝐦𝐞𝐦𝐛𝐫𝐚𝐧𝐞 -𝐥𝐢𝐩𝐢𝐝𝐬 𝐏𝐎𝐏𝐂 60 𝐏𝐎𝐏𝐄 35 𝐃𝐃𝐏𝐂 5 The video shows the creation of a 20 nm^2 membrane of the following composition: POPC 50%, DMPC 40%, cholesterol 10%. In the video you see about 700 lipids (fat molecules) being spawned far from each other, to ensure none are overlapping. They are then rapidly pushed towards the center of a box, while running a Molecular Dynamics simulations, to ensure the lipids clump together realistically. Then as the simulation pauses, the monolayer is mirrored, making it a bilayer membrane (which is exactly what surrounds our cells), and a short simulation is run to "relax" the membrane. *The current version is mainly promotional, quite unstable and won't generate a completely physically accurate membrane. Thanks for reading. Stay tuned for more updates on the development. /Daniel

#Devlog 5: Membrane builder, interactive live-previews and more The development of LIMA continues rapidly. The newest feature is a fast membrane builder, for which you can see the prototype in the video below. To simplify implementation, we have developed some quality-of-life tools., including the ability to see a live-preview of the simulation, which can be rotated to better understand what is happening in the simulation. Additionally we have made a tool to reorder the atom-nr of gro/top files, to make showing part of molecules in VMD or other visualizers easier. While this is currently just a prototype on the development branch, we will make the features public within the next 2 weeks, so stay tuned for more updates. /Daniel Video: The Membranebuilder algorithm in live action. First a group of POPC lipids are distributed evenly in a grid. They are then rapidly pushed towards the simulation-box, while running a live Energy Minimizing MD simulation. Once all molecules are within the box, the layer is mirrored to create a bilipid membrane. A short MD simulation with Periodic Boundary Condition is then run to let the membrane settle.