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Hi, I found two problems when performing molecular dynamics simulations using MACE-OPENMM.
1. Multiple GPU cards can be applied without error. But there is only one GPU card running the operation.
2…
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The file format should support common input and output for these applications:
At minimum:
1. Molecular dynamics: simulation (OpenMM, DESMOND, etc.) and analysis packages (MDTraj, PyTraj, etc.)
2. Qu…
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## New Use Case
Aspect | Detail
------------ | -------------
Summary | C1997 (Platforms providing web-access to molecular level tools for guiding systems level modelling)
Usecase Group | Molec…
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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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**Submitting author:** @bobleesj (Sangjoon Lee)
**Repository:** https://github.com/bobleesj/cifkit
**Branch with paper.md** (empty if default branch): JOSS
**Version:** v1.0.2
**Editor:** @rkurchin
**…
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Hi, the example about the QM9 database is very illustrative for me to perform regression of molecular properties on my own dataset.
¿It would be possible to implement the computation of the deriva…
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Instead of implementing ES logic externally we prefer to use GROMACS to do this. This should reduce bugginess, instability and complexity.
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Zhang et al. 2021 (https://doi.org/10.1038/s41427-021-00320-0):
This paper has reviewed several simulations to study the interaction of nanoparticles (NPs) and membrane. This paper said there are se…
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**Aim:**
This issue addresses how to apply LigGrep to filter through docked ligand poses to check that they retain key interactions with the protein that are observed in crystallographic fragment-p…
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