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Funnel meta-dynamics, is meta-dynamics where we restrain ligand in a cone/cylinder-shaped potential, where the ligand expriences potential K, when outside cone/cylinder and no potential when inside. I…
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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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The biasing potential in metadynamics is controlled by the MD step number. This means that the biasing potential gets switched on instantaneously when a small time step is used, resulting in the syste…
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This issue is for the discussion of the second problem, which is mainly about the strategies for deciding simulation parameters for 2D alchemical metadynamics for the CB8-G3 system.
Briefly, the q…
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Greetings, I am interested in reproducing the results you obtained. I am running the notebook _"SML_CV-master/alanine_example/01-svm_example.ipynb"_. However, I cannot resolve the following error:
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Thanks for your response to my original question. I did look at getFreeEnergy, which makes so much more sense than reading the npy file from the biasDir as I was doing earlier.
I was hoping to save…
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Dear SSAGES developers,
I want to calculate the free energy using the ANN method.
The following is the content of a JSON file used in ANN:
```json
{
"walkers" : 1,
"input" : "in.met…
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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 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…