Questions tagged [openpathsampling]

Questions about the OpenPathSampling (OPS) software for path sampling methods, such as transition path sampling (TPS) and transition interface sampling (TIS).

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2 votes
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Adding new CVs to a Storage

I am trying to add a new CV (A plumed one) to a storage. I've completed a TPS simulation, and now I want to store the new CV for later analysis use. ...
user avatar
3 votes
0 answers

OpenMM engine options in openpathsampling (OPS) python library

Context: I'm new to OpenMM and transition path sampling (TPS). I tried to set up a two-state TPS with the openpathsampling python library using the flexible length ...
Kui's user avatar
  • 31
5 votes
1 answer

trajectory_from_mdtraj requires simtk.unit, which is not installed

I am trying to load my MD trajectory to postprocess the velocities. Although I use the same exact script on the OPS website, I get the following error: ...
Hana Oliaei's user avatar
7 votes
1 answer

How do I setup my MSTIS simulation correctly?

I'm trying to setup a Multi State Transition Interface Sampling (MSTIS) simulation to study the ligand binding of my enzyme using OPS and GROMACS. My enzyme acts on small sugar chains and I would like ...
Martin Bonin's user avatar
7 votes
2 answers

Import an initial trajectory into OPS without OpenMM

I'm trying to use openpathsampling to simulate the binding of a ligand to my enzyme. I'm using Gromacs for my normal simulation on the HPC system provided by my university. I created an initial ...
Martin Bonin's user avatar
6 votes
1 answer

How is the atom selection going wrong when creating the collective variable?

I'm trying to create a CV for angle theta. To make this calculation, the right atom selections need to be made. The function is given below: ...
rika-27's user avatar
  • 115
5 votes
1 answer

How do I select atoms using mdtraj_topology when creating a CV?

I am adding a new collective variable (CV) that I will use to calculate a path density with OpenPathSampling. I played around a bit with the CVs and I have one error that I'm not sure how to fix. I'm ...
rika-27's user avatar
  • 115
11 votes
0 answers

Setting multiple new atype/dtype/itype with LAMMPS fix bond/create [closed]

When creating a new bond in a LAMMPS simulation with the command fix/bond create it is likely new angles/dihedrals/impropers be need to be set. This can be done with the atype/dtype/itype arguments ...
Matt's user avatar
  • 341