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I have a system that is a protein with a cofactor (FAD).
I am trying to generate the topology for this system.
In particular I am trying to do this:
Importing the topology for the ligand from a gro…
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In setting up a variety of systems for simulation I came across one with a thioether bond (something I haven't encountered before in a protein I'm trying to simulate). The PDB structure is https://www…
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My openmm script is running fine with openmm=7 (specifically 7.6 and 7.7) but showing "particle coordinate is naN" in openmm=8. I have used the pdb attached below. The issue is happening for both mini…
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AFAIK we're not leveraging any new features, but compatibilities might cause issues for users at install time.
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Known upstream blockers
- [ ] Pint
- [ ] OpenMM https://github.com/openmm/o…
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Hi all,
I was wondering if is possible to add the support for the AMD HIP platform.
Specifically OpenMM already is able to work on HIP platforms installing a specific hack with Conda:
`mamba in…
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Hi,
I am new to the AMOEBA force filed. I am using poltype2 to generate amoeba force field. Is there any tools to convert easily the thinker format to openmm xml? Also, I found a script from github w…
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I am not sure if this is a known issue, but I noticed that CVs which rely on the barycenter has a small issue in OpenMM.
To my knowledge, OpenMM wraps particle coordinates internally when using PBC…
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We currently have three different pdb writers (OpenMM, mdtraj and chemfiles).
All of them have different characteristics regarding performance and compability, so I would like to keep them around.
…
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Hello,
We are running Alphafold 2.3.1 on a Linux HPC through SLURM submission. The databases were downloaded to our cluster for AF2 to run correctly. We were able to successfully run 2.2.4, but w…
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I just saw a talk referencing another "ACEMD". Just for info: https://www.acellera.com/acemd.