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Proteins have characteristic secondary structure (https://en.wikipedia.org/wiki/Protein_secondary_structure)
The PDB format has a section for specifying secondary structure (https://www.wwpdb.org/d…
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The `mda.coordinates.TRJ.NCDFReader` expect an Amber-generated NetCDF trajectory to have `time` information in the `variables` object of the NetCDF file.
This is true for NetCDF files created by AMB…
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Most routines will automatically be GPU friendly, simply by leveraging torch's GPU structure. Some will not, however. In particular, I've gotten complains from plotting infrastructure, such as `tdg.…
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**Submitting author:** @amiralih (Amirali Hossein)
**Repository:** https://github.com/amiralih/MembraneAnalysis.jl
**Branch with paper.md** (empty if default branch):
**Version:** v0.3.2
**Editor:** …
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I get illegal instruction when trying to load *any* of my XYZ files;
```
[12:48:22][debug]: Initializing GL... [/home/sandervandenhaute/viamd/src/main.cpp:1336]
[12:48:22][debug]: Initializing fr…
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Hello,
I want to use multiple gpus with the ReplicaExchangeSampler and MultiStateReporter to produce trajectories for an HREMD simulation. Although the system appears to get setup properly and the…
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Hello, I have a question about the capabilities of mfem regarding a problem I want to solve.
I want to design a device to guide molecular ions with electrodes (as in ion optics), I would like to know…
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The order parameters for POPC acyl chain with CHARMM36 model are larger than in experiments in figure https://github.com/NMRLipids/NmrLipidsCholXray/blob/master/FIGS/OrderParametersCHOL.jpg.
The resul…
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I am using voro++ in a program for analysis of molecular dynamics trajectories (i.e. 3D coordinates). The main part involves calculating Voronoi cells for each atom, and then determining the density o…
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Problem: Several gromacs tests fail after rebasing NOMAD.
More specifically, line 1094 of parser.py in gromacs/ throws an error having to do with converting a str input parameter like '0 0 …