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These files only contain topology information and seem to be widely used in bio-molecules simulations.
See here for a description: https://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix…
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As a followup on my PR #1709, there were tools in workflows I could not attach the correct tool_shed_repository to:
Topic | Tutorial | Tutorial name | Tutorial file name | Tool name [Tool id] t…
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I'm currently attempting to convert parameters generated with CGenFF into a gromacs usable form, but am running into some issues. CGenFF returns a .str and .mol2 file rather than a .psf and .crd. Both…
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Hi all,
I've been using polyply with Martini 3 parameters to create some simulation systems of variable length line polymer solutions. I'm happy to say that CEL and DEX parameters worked very nicel…
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Hi all,
Our lab has tried to use the GaMD-OpenMM code to simulate CHARMM36 systems but the stock code seems to be not working for them. @hmmichel has been working on this as well.
The first issu…
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Hi,
I am testing OpenMM multi-GPU performance. The result shows that simulation speed using 2 GPUs (5.80 ns/day) is slower than 1 GPU (6.75 ns/day). We use the NVIDIA RTX A40 GPUs and the jobs were…
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Dear developers,
I came across this situation, and I'm not absolutely certain it is an issue with pdb2pqr, but I thought it would be nice to inform.
It happened when preparing a protein (pdb id:…
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@sef43 @peastman @raimis : Here's my proposal for next steps with the openmm-cookbooks repo:
- [x] **Change the colab link to be URL-aware:** Currently, the [google colab link](https://github.com/ope…
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Dear OpenMM Development Team,
I hope you could find the discrepancy I've discovered in the implementation of the Reaction Field (RF) formula between OpenMM and GROMACS, which potentially leads to s…
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Related to #247 - currently Yank has systembuilder, which probably ought to be split off into a more general-purpose tool that will be useful aside from just for Yank workflows (i.e. setup of GROMACS …