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@isuruf it looks like all of the failure in CI are due to duplicate assets, does that mean we need more unique file names? or does it mean that our matrix needs to be trimmed down? I know on conda-for…
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Hello OpenMM users!
I am facing a problem during script running in openmm. Whenever I have tried to run the openmm script, so at each time it gives me the error "OpenMMException: No compatible CUDA d…
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I wish to utilize the amber99sb-disp force field in OpenMM, which is proficient in describing Intrinsically Disordered Proteins (IDPs). I intend to combine it with OpenMM's metadynamics to accelerate …
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- How should one protonate the ligand?
- How should one add partial charges to the ligand (i.e. AMBER vs OpenEye)
- How one generate forcefield parameters for ligands for (a) explicit solvent and (b) …
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Dear OpenMM team,
I am looking for a package/tutorial to do protein-protein binding free energies. I have found plenty of alchemical methods for protein-ligand but none for protein-protein. Any poi…
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When I try to simulate glycans with Openmm using the script below, I get the error I mentioned at the bottom. Is there a solution for this or is it due to a lack of development in forcefield in the XM…
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I've just realized that the [latest API docs](http://docs.openmm.org/latest/api-python/) don't mention which version of OpenMM they are for, and methods and classes don't indicate which version they w…
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Dear OpenMM experts,
I am trying to run a simple simulation with a protein and ligand, followed by a binding free energy calculation of the docked ligand (NADPH).
To do this, I am first building t…
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The input script for the [Beta-2-adrenergic receptor (B2AR) membrane protein simulation with CHARMM](http://openmm.org/tutorials/b2ar_membrane/) tutorial apparently contains several errors:
`# Load…
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The Openmm Metadynamics source code has the following line:
`position = self._force.getCollectiveVariableValues(simulation.context)`
The CV values obtained from this are not matching with those foun…