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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…
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I have some queries regarding `RawPositionsFeaturizer`
1. If I want to use atom indices as mentioned in the document like `RawPositionsFeaturizer(atom_indices=None, ref_traj=None)`. Is the followin…
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In setting up a metadynamics simulation with a system and state file, I was hoping to be able to setup a simulation using a dihedral and a pair of distances as my collective variables. However, when I…
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In the trajectory file from a metadynamics run, the potential energy printed is the "full" metadynamics energy, including the RMSD bias potential (and possibly also reactor wall potential). For analys…
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Hi All,
We've had good success running metadynamics simulations starting from parmed objects, but have noticed that some percentage of the runs (
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I am running an AIMD Metadynamics calculation using cp2k for a small system (89 atoms and 256 electrons). I also have PLUMED patched for enabling Metadynamics calculations. The calculations would run …
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Hi PySAGES developers, first thank you again for the nice code!
I've seen some codes regarding JAX-MD as backend simulator, but have not yet figured out how I could use it for metadynamics. Does PyS…
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Upon doing the Alanine Dipeptide tutorial given on openpathsampling website using GROMACS, all the steps I have done like what it is showing in the tutorial. All the steps up to committor analysis wer…
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Does openmm-torch support multivariate collective variables? I would like to do metadynamics along an NN collective variable in 3 dimensions, and the current openmm-torch documentation involves only u…
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Add a section to showcase papers that use this software.