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125w system with case2 fixed, 15ps sub-trajectory. Wrong results. Don't know why
Fig. 3, 4, 5 seem all wrong. The solid and dashed data are overlapped. Still debugging where is the prob…
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Dear Shankar
In jdftx settings, setting both 'ionic-dynamics' and 'target-mu' parameters as below command line
```
ionic-dynamics \
dt 2 \
nSteps 5000 \
statMethod NoseHoover…
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If you are using Zarr for whatever purpose, we would love to hear about it. If you can, please leave a couple of sentences in a comment below describing who you are and what you are using Zarr for. Th…
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It could be useful to support simulations with explicit space group symmetry, along the lines of http://pubs.acs.org/doi/abs/10.1021/ct100506d. I think this could be done with just another type of vi…
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there are a lot of tools that parse LaTeX, but unsure of how easy it is to reliably extract logical groupings of TeX.
To narrow the scope of the survey, exclude tools that rely on conversion to so…
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Dear authors,
We have been using DSSP to analyze molecular dynamics simulations. We have wrapped it into [a package](https://m3g.github.io/ProteinSecondaryStructures.jl) that performs this analysis…
lmiq updated
4 months ago
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Please find below a conversation with @ceriottm , who kindly agreed (suggested, actually) to share this here as a record of the reasoning behind the current scope of the `atomistic.software` list and …
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Dear OpenMM-ML developers,
I've been successfully using OpenMM-ML to utilize MACE potentials for molecular dynamics simulations with MACE versions 0.2.x. However, after upgrading MACE to version 0.…
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I redid the calculations for the exact solution and did a simple test case with 600000 fake samples in 4 TIS ensembles and using pymbar and my formula to compute the `f_k` "free_energies" of the ensem…
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Hello!
At the moment, Foyer can generate only `*.top` and `*.gro` files for GROMACS simulations. However, it would be useful also to add support for the users of other Molecular Dynamics packages, …