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AmartyaRewrote the existing C code for a simple molecular dynamics simulation in Rust. What a brilliant language. So clean and clear. Fun experience. Took me 3 days. (No LLM help haha).<a href="https://codeberg.org/amartya/MolDyn_Rust" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://codeberg.org/amartya/MolDyn_Rust</a><a href="https://fosstodon.org/tags/rustlang" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rustlang</a> <a href="https://fosstodon.org/tags/rust" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#rust</a> <a href="https://fosstodon.org/tags/c" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#c</a> <a href="https://fosstodon.org/tags/moldyn" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#moldyn</a> <a href="https://fosstodon.org/tags/moleculardynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#moleculardynamics</a> <a href="https://fosstodon.org/tags/learning" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#learning</a> <a href="https://fosstodon.org/tags/programming" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#programming</a> <a href="https://fosstodon.org/tags/cpp" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cpp</a> <a href="https://fosstodon.org/tags/llm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#llm</a>

LavX NewsUnlocking Performance: Benchmarking Molecular Dynamics Simulations with Advanced Compiler OptimizationsIn the realm of scientific computing, the efficiency of molecular dynamics simulations can make or break research outcomes. This article delves into the intricacies of benchmarking a calcium aluminosi...<a href="https://news.lavx.hu/article/unlocking-performance-benchmarking-molecular-dynamics-simulations-with-advanced-compiler-optimizations" rel="nofollow noopener noreferrer" target="_blank">https://news.lavx.hu/article/unlocking-performance-benchmarking-molecular-dynamics-simulations-with-advanced-compiler-optimizations</a><a href="https://mastodon.cloud/tags/news" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#news</a> <a href="https://mastodon.cloud/tags/tech" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#tech</a> <a href="https://mastodon.cloud/tags/ScientificComputing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ScientificComputing</a> <a href="https://mastodon.cloud/tags/MolecularDynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MolecularDynamics</a> <a href="https://mastodon.cloud/tags/CompilerOptimizations" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CompilerOptimizations</a>

Piia BartosRunning 16 simulations in parallel is a very efficient way of making simulations. It sucks however, that they all crash if one of them crashes. <a href="https://mastodontti.fi/tags/simulation" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#simulation</a> <a href="https://mastodontti.fi/tags/compchem" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#compchem</a> <a href="https://mastodontti.fi/tags/molecularDynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#molecularDynamics</a> <a href="https://mastodontti.fi/tags/MolecularModeling" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MolecularModeling</a>

Markus OsterhoffYoung Scientist Award:Petrick Heighwayfor his pivotal role in the DiPOLE-100x Community Proposals measuring <a href="https://academiccloud.social/tags/XRay" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#XRay</a> <a href="https://academiccloud.social/tags/diffraction" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#diffraction</a> at extreme pressures and temperatures at the HED-HiBEF instrument.Combines experimental data with <a href="https://academiccloud.social/tags/MolecularDynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MolecularDynamics</a> simulations to provide critical insight into the nature of release pathways of shock compressed materials, kinematics of plastisticy, …<a href="https://academiccloud.social/tags/UM25" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#UM25</a> <a href="https://academiccloud.social/tags/EuropeanXFEL" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#EuropeanXFEL</a>

G. ClavierI am shamefully copying this post from Linkedin but if you happen to know any candidate, do not hesitate to reach:It's on. To my <a href="https://social.sciences.re/tags/ComputationalChemistry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ComputationalChemistry</a> network, I am calling on you. 🙇 The PM2E team in the CIMAP laboratory (www.cimap.ensicaen.fr) is looking for a <a href="https://social.sciences.re/tags/PhD" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#PhD</a> hashtag#candidate. The goal of the project is to understand key parameters in <a href="https://social.sciences.re/tags/semiconductor" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#semiconductor</a> defects stability and physics (both vacancies and color centers, see for example: <a href="https://doi.org/10.1016/j.nimb.2022.12.025" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://doi.org/10.1016/j.nimb.2022.12.025</a>) through the use of <a href="https://social.sciences.re/tags/DFT" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#DFT</a> and <a href="https://social.sciences.re/tags/MolecularModeling" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MolecularModeling</a>. The end goals of the project is concerned with application for <a href="https://social.sciences.re/tags/QuantumComputing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#QuantumComputing</a> through the making of stable <a href="https://social.sciences.re/tags/qubit" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#qubit</a>. Collaboration and communication with experimentalists will be part of the project.If you're interested in <a href="https://social.sciences.re/tags/MolecularDynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MolecularDynamics</a>, <a href="https://social.sciences.re/tags/MonteCarlo" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MonteCarlo</a> simulations, or DFT and quantum calculations, we are waiting for you. We are using codes such as <a href="https://social.sciences.re/tags/Lammps" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Lammps</a> and <a href="https://social.sciences.re/tags/QuantumEspresso" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#QuantumEspresso</a>. We are looking for a candidate finishing or already having a master degree (or equivalent diploma) with training in <a href="https://social.sciences.re/tags/physics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#physics</a>/ <a href="https://social.sciences.re/tags/MaterialsScience" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MaterialsScience</a> / <a href="https://social.sciences.re/tags/TheoreticalChemistry" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#TheoreticalChemistry</a>. Any experience in programming using <a href="https://social.sciences.re/tags/Python" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Python</a>, <a href="https://social.sciences.re/tags/C" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#C</a> and the <a href="https://social.sciences.re/tags/Linux" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Linux</a> environment would be considered a plus.The position is located in Alençon (Orne) between Caen and Le Mans. Founding is assured for relevant candidates.Link to the offer (in french, you can ask for an english version): <a href="https://www.abg.asso.fr/en/candidatOffres/show/id_offre/127985/job/simulation-atomistique-de-defauts-crees-par-irradiation-dans-les-semiconducteurs" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://www.abg.asso.fr/en/candidatOffres/show/id_offre/127985/job/simulation-atomistique-de-defauts-crees-par-irradiation-dans-les-semiconducteurs</a>

RJ NowlingTrying to get back in the <a href="https://mastodon.social/tags/moleculardynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#moleculardynamics</a> bandwagon. Found a <a href="https://mastodon.social/tags/NMR" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NMR</a> structure for a relatively small neurotoxin protein bound to a small peptide that neutralizes it. No one seems to have done any MD simulations yet. Started some sims. Maybe I’ll observe something interesting worth publishing.

Keiran RowellOkay, who snuck in a <a href="https://mastodon.social/tags/Tricky" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Tricky</a> quote into <a href="https://mastodon.social/tags/GROMACS" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#GROMACS</a> ?!<a href="https://youtu.be/nDYeb6PeixQ" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://youtu.be/nDYeb6PeixQ</a><a href="https://mastodon.social/tags/triphop" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#triphop</a> <a href="https://mastodon.social/tags/moleculardynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#moleculardynamics</a> <a href="https://mastodon.social/tags/scientificcomputing" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#scientificcomputing</a>

Pete CarltonIs anyone doing structure prediction with <a href="https://fediscience.org/tags/AlphaFold3" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#AlphaFold3</a> figured out an easy way to do the relaxation step that Colabfold did? I'm looking into OpenMM and Amber, and making some progress, but it seems like it will be very difficult to make it work when phosphoresidues, ions, or anything else besides standard amino acid residues are included.<a href="https://fediscience.org/tags/proteins" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#proteins</a> <a href="https://fediscience.org/tags/structuralbiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#structuralbiology</a> <a href="https://fediscience.org/tags/moleculardynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#moleculardynamics</a>

Keiran RowellThe D. E. Shaw Research DNA/RNA <a href="https://mastodon.social/tags/moleculardynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#moleculardynamics</a> force-fields look great. These non-canonical DNA structures are beautiful. Observing B-DNA <-> Z-DNA inter-conversion during simulation is so cool.G-quadruplexes are such neat compact bundles.The deficiencies are in nucleic acid-protein interactions -- getting values from different force-fields to play nice and be consistent is hard.• Paper: <a href="https://pubs.acs.org/doi/10.1021/acs.jpcb.1c10971" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://pubs.acs.org/doi/10.1021/acs.jpcb.1c10971</a> • Force-field code: <a href="https://github.com/DEShawResearch/viparr-ffpublic" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://github.com/DEShawResearch/viparr-ffpublic</a> <a href="https://mastodon.social/tags/structuralbiology" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#structuralbiology</a>

Keiran Rowell<a href="https://pubs.acs.org/doi/10.1021/acs.jctc.4c00773" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://pubs.acs.org/doi/10.1021/acs.jctc.4c00773</a>A great summary of the current improvement in <a href="https://mastodon.social/tags/RNA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#RNA</a> force-fields in <a href="https://mastodon.social/tags/moleculardynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#moleculardynamics</a>, with a table of applied case studies and a section on incorporating experimental data

HGPU groupIn-Situ Techniques on GPU-Accelerated Data-Intensive Applications<a href="https://mast.hpc.social/tags/CUDA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CUDA</a> <a href="https://mast.hpc.social/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> <a href="https://mast.hpc.social/tags/Performance" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Performance</a> <a href="https://mast.hpc.social/tags/MolecularDynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MolecularDynamics</a><a href="https://hgpu.org/?p=29336" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://hgpu.org/?p=29336</a>

HGPU groupRBMD: A molecular dynamics package enabling to simulate 10 million all-atom particles in a single graphics processing unit<a href="https://mast.hpc.social/tags/CUDA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CUDA</a> <a href="https://mast.hpc.social/tags/MolecularDynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MolecularDynamics</a> <a href="https://mast.hpc.social/tags/Physics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Physics</a> <a href="https://mast.hpc.social/tags/Package" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Package</a><a href="https://hgpu.org/?p=29302" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://hgpu.org/?p=29302</a>

SantiagoPara los que estuvieron en mi charla en la FLISoL sobre clústers de cálculo numérico, hoy largamos 729 simulaciones de 3000 partículas al clúster de una, más o menos esperamos que el mismo complete 10 corridas por día, por lo que en unos 73 días tendríamos los resultados <a href="https://mastodon.uy/tags/hpc" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#hpc</a> <a href="https://mastodon.uy/tags/cluster" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cluster</a> <a href="https://mastodon.uy/tags/ciencia" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#ciencia</a> <a href="https://mastodon.uy/tags/md" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#md</a> <a href="https://mastodon.uy/tags/dinamicamolecular" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#dinamicamolecular</a> <a href="https://mastodon.uy/tags/moleculardynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#moleculardynamics</a> <a href="https://mastodon.uy/tags/science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#science</a> <a href="https://mastodon.uy/tags/fisica" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#fisica</a> <a href="https://mastodon.uy/tags/physics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#physics</a>

HGPU groupGaining Cross-Platform Parallelism for HAL’s Molecular Dynamics Package using SYCL<a href="https://mast.hpc.social/tags/SYCL" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SYCL</a> <a href="https://mast.hpc.social/tags/CUDA" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#CUDA</a> <a href="https://mast.hpc.social/tags/Physics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Physics</a> <a href="https://mast.hpc.social/tags/MolecularDynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MolecularDynamics</a> <a href="https://mast.hpc.social/tags/Package" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Package</a><a href="https://hgpu.org/?p=29239" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://hgpu.org/?p=29239</a>

EnthalpisteJ'ai fait une petite simulations rigolote pour vérifier numériquement un vieux truc que j'ai trouvé dans un article de Boltzmann. Si on met une particule dans un plan avec deux ressorts qui ont des constantes de forces k1 et k2, la trajectoire est périodique si k1/k2 est un nombre rationnel: <a href="https://youtu.be/keGGbb2uiB8" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://youtu.be/keGGbb2uiB8</a>Évidemment si c'est pas un nombre rationnel (genre pi), c'est pas périodique: <a href="https://youtu.be/Tty0jFWKkv8" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://youtu.be/Tty0jFWKkv8</a>Voilà, c'est tout pour moi.<a href="https://mastodon.xyz/tags/Physics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Physics</a> <a href="https://mastodon.xyz/tags/Boltzmann" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Boltzmann</a> <a href="https://mastodon.xyz/tags/lammps" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#lammps</a> <a href="https://mastodon.xyz/tags/MolecularDynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MolecularDynamics</a>

HGPU groupGROMACS on AMD GPU-Based HPC Platforms: Using SYCL for Performance and Portability<a href="https://mast.hpc.social/tags/Physics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Physics</a> <a href="https://mast.hpc.social/tags/MolecularDynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MolecularDynamics</a> <a href="https://mast.hpc.social/tags/HPC" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#HPC</a> <a href="https://mast.hpc.social/tags/Performance" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Performance</a> <a href="https://mast.hpc.social/tags/SYCL" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#SYCL</a> <a href="https://mast.hpc.social/tags/Package" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Package</a><a href="https://hgpu.org/?p=29198" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://hgpu.org/?p=29198</a>

jobRxivMolecular dynamics and multiscale modelling for sustainability DAIMON Team - CNR-ISMNFull time researcher in <a href="https://mas.to/tags/moleculardynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#moleculardynamics</a> and <a href="https://mas.to/tags/multiscalemodelling" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#multiscalemodelling</a> for sustainable materials @CNR-ISMN Bologna, Italy <a href="https://mas.to/tags/Gromacs" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Gromacs</a> <a href="https://mas.to/tags/LAMMPS" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#LAMMPS</a>See the full job description on jobRxiv: <a href="https://jobrxiv.org/job/daimon-team-cnr-ismn-27778-molecular-dynamics-and-multiscale-modelling-for-su" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://jobrxiv.org/job/daimon-team-cnr-ismn-27778-molecular-dynamics-and-multiscale-modelling-for-su</a>... <a href="https://jobrxiv.org/job/daimon-team-cnr-ismn-27778-molecular-dynamics-and-multiscale-modelling-for-sustainability/?feed_id=69895" rel="nofollow noopener noreferrer" translate="no" target="_blank">https://jobrxiv.org/job/daimon-team-cnr-ismn-27778-molecular-dynamics-and-multiscale-modelling-for-sustainability/?feed_id=69895</a>

ScietyA significant challenge of biomolecular simulations are the computational limitations. A new method aims to overcome these by employing <a href="https://fediscience.org/tags/Bayesian" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#Bayesian</a> neural network learning models.More details in the <a href="https://fediscience.org/tags/preprint" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#preprint</a> evaluated on <a href="https://mas.to/@prereview" class="u-url mention" rel="nofollow noopener noreferrer" target="_blank">@prereview</a> <a href="https://fediscience.org/tags/NeuralNetwork" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#NeuralNetwork</a> <a href="https://fediscience.org/tags/MolecularDynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MolecularDynamics</a><a href="https://sciety.org/articles/activity/10.1101/2023.03.25.534210?utm_source=mastodon&utm_medium=social&utm_campaign=sci_mastodon_2023_111" rel="nofollow noopener noreferrer" target="_blank">https://sciety.org/articles/activity/10.1101/2023.03.25.534210?utm_source=mastodon&utm_medium=social&utm_campaign=sci_mastodon_2023_111</a>

SantiagoFinalmente terminé de reinstalar todo el cluster de dinámica molecular, ahora tenemos una PC más. Ahi se ve corriendo el LAMMPS en 56 procesadores con Slurm WorkLoad Manager y OpenMPI <a href="https://mastodon.uy/tags/cluster" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#cluster</a> <a href="https://mastodon.uy/tags/md" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#md</a> <a href="https://mastodon.uy/tags/slurm" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#slurm</a> <a href="https://mastodon.uy/tags/moleculardynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#moleculardynamics</a> <a href="https://mastodon.uy/tags/udelar" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#udelar</a> <a href="https://mastodon.uy/tags/uruguay" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#uruguay</a>

EnthalpisteHappy to see another command I worked on merged in the LAMMPS code.Langevin barostat is now available to use, thanks to the dev team which is of very wise help.Waiting for users feedback, if any. 😊<a href="https://mastodon.xyz/tags/science" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#science</a> <a href="https://mastodon.xyz/tags/lammps" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#lammps</a> <a href="https://mastodon.xyz/tags/MolecularSimulation" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MolecularSimulation</a> <a href="https://mastodon.xyz/tags/MolecularDynamics" class="mention hashtag" rel="nofollow noopener noreferrer" target="_blank">#MolecularDynamics</a>

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