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Velocity Verlet is the most used integration method and used in all/most molecular dynamics packages, physics simulations and games.
http://en.wikipedia.org/wiki/Verlet_integration#Velocity_Verlet
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[H5MD](http://nongnu.org/h5md/h5md.html) is a specification for an output format used for storing results from molecular dynamics simulations. It describes the layout (groups/datasets and attributes) …
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**Summary**
As the title says
**Detailed Description**
According to the documentation: https://docs.lammps.org/Speed_gpu.html, FFT uses CPU to take advantage of MPI communication between proc…
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[Hou, Tingjun, Junmei Wang, Youyong Li, and Wei Wang. “Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Sim…
cramg updated
3 years ago
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This issue is to discuss the possibility of adding path integral methods to the already existing classical MD / MC framework. Quantum-classical isomorphism enables mapping of the thermodynamics of a …
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Take this paper: https://dissem.in/p/131996/molecular-dynamics-simulations-of-electronalkali-cation-pairs-in-bulk-water which is correctly linked to HAL: https://hal.archives-ouvertes.fr/hal-00088127 …
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[Maruca, Annalisa, Francesca Alessandra Ambrosio, Antonio Lupia, Isabella Romeo, Roberta Rocca, Federica Moraca, Carmine Talarico, et al. “Computer-Based Techniques for Lead Identification and Optimiz…
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I just want to find a link to SSAGES.jl to add it to timestamps for [_Enhanced Sampling in Molecular Dynamics Simulations with Julia_ ](https://www.youtube.com/watch?v=a6sciHRP6m) and I landed here. T…
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At the moment, we can only take ranges with a step of 1, but it would be useful to reduce sets by taking steps of e.g. 10, 100 or 100.
Perhaps, we could extend the syntax to include something like …
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is:issue is:open Hello! My name Zhukov Vladlen, I am Phd student. I tried to reproduced your supplementary. https://doi.org/10.1016/j.commatsci.2020.109951 But I came across a problem - the atoms in t…