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Files from https://acs.figshare.com/articles/dataset/Small_Molecule_Solvation_Free_Energy_Enhanced_Conformational_Sampling_Using_Expanded_Ensemble_Molecular_Dynamics_Simulation/2615170 have some issue…
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Hi @yury-lysogorskiy
I am currently exploring to use the PACE framework to predict the thermal conductivity of AlGaN alloys using the Green-Kubo method (by performing equilibrium molecular dynamic…
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**Submitting author:** @pw0908 (Pierre Walker)
**Repository:** https://github.com/bbye98/mdcraft
**Branch with paper.md** (empty if default branch): main
**Version:** v1.1.0
**Editor:** @srmnitc
**Rev…
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[GROMACS tutorial](http://www.mdtutorials.com/gmx/complex/01_pdb2gmx.html )
[GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design](https://doi.org/10.1021/acs.jcim.2c0004…
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Hello!
Thank you very much for the tutorial on the topology builder.
Is it possible to generate a periodic graphene oxide topology for molecular dynamics
simulation or can only a finite to…
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Hello, I will be conducting molecular dynamics for several protein-ligand complexes. Is it possible to calculate the interaction energy between the protein and the ligand for individual simulation ste…
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### Details
Running molecular dynamics simulations of Ti(0001) surface under NVT ensemble using Abacus software. The total timestep is set to 500 steps, but the simulation unexpectedly terminates aft…
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# Problem
Given a set of 3D points (particles) and a radius, for every particle find all particles within a sphere of the given radius.
Of note:
- Finding extra particles outside of the sphere…
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Greetings,
I'm Marco Ravalli, a phD student working on molecular dynamics by classical interatomic potentials. I'm currently trying to use one of the pretrained MACE models to work with my systems, …
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### Details
The computational system is the Ti metal (001) surface containing 72 atoms, and molecular dynamics simulations were performed on it with a timestep of 500 steps and a frequency of 1 fs. T…