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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5
votes
1answer
42 views

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 ...
7
votes
2answers
116 views

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 ...
6
votes
1answer
84 views

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: ...
5
votes
1answer
135 views

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 ...
11
votes
0answers
114 views

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 ...