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In this [line](https://github.com/pandegroup/pdbfixer/blob/699ba1033a46c2a862f4cce0f271c37667677f07/pdbfixer/pdbfixer.py#L513)
newResidue = chain.topology.addResidue(residueName, chai…
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I'd like some feedback on how to handle errors for when a core encounters a NaN, insane forces, or has a major Force discrepancy with the Reference platform. These are all symptoms of one or more of t…
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The Charmm forcefield includes elements for improper dihedrals (which are supported in OpenMM and ParmEd). Foyer needs to accept CustomTorsionForce elements also
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Hi,
I would calculate the hydration free energy of ethanol using OpenMM with CHARMM Drude force field but I don't know how to do that. My questions are: does Yank work with the Drude FF?
If you ha…
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After discussing with @jchodera - and building on #218 - Is there any plans to add phosphorylated residues such as pSer and pTyr as templates? For setting up initial structures for OpenMM simulation, …
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Please add cuda DeviceIndex settings, similar to the Openmm Platform module, for easy operation on multi graphics card machines
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I am trying to test OpenMM-7.6.0 on a new server ( GPU: NVIDIA GeForce RTX 3090). OpenMM was installed using the miniconda3 package manager:
```
conda create --name openmm python=3.7
conda activa…
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For certain molecules, like the phenylformate example here:
[phenylformate.zip](https://github.com/openmm/openmm-ml/files/9490903/phenylformate.zip)
I get an error when creating a mixedSystem:
`ml_…
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From @peastman:
> Rather than using global parameters for the constants, I suggest hardcoding them in the expression. That is, add softcore_alpha=0.5; softcore_a=1; softcore_b=1; softcore_c=6 to your…