OpenMM WESTPA

[Sreyoshi Sur]

Hi,

I am trying to use OpenMM in WESTPA. The problem I am running into is conflict of python 3.6 in which OpenMM runs and python 2.7 in which WESTPA runs.

Has anyone worked with the newer OpenMM and WESTPA.Any inputs regarding this issue will be greatly appreciated.

Thanks

Sreyoshi Sur

Ph.D. candidate

University of Rochester

[Matthew Zwier]

Sreyoshi,

WESTPA is currently being updated for Python 3. It's not ready yet. Is there a version of OpenMM available that runs on Python 2.7?

Cheers,

Matt Z

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[Sreyoshi Sur]

Hi Matt,

I was trying to run this system on our cluster, Bluehive, which already had a OpenMM 7.2 build with python3. So I installed my own OpenMM now in the WESTPA environment with both CUDA and OpenCL platforms. The NaCl example works now.

I was wondering if anyone has another OpenMM example with a little complicated system working. I am trying to adapt the openmm_propagator.py in the NaCl tutorial to my system which involves multiple basis states and a customized progress coordinate calculation.

Thanks

Sreyoshi Sur

Ph.D. candidate

University of Rochester

[Lillian Chong]

Hi Sreyoshi,

Having an updated WESTPA tutorial using OpenMM has been on our list, but we won't be able to get to it until WESTPA has been updated to Python 3.

In the meantime, you may find this tutorial for using either MDAnalysis or MDTraj for calculating progress coordinates useful:

https://github.com/westpa/westpa/wiki/Calculating-Progress-Coordinates-with-MDAnalysis-and-MDTraj

Best,

Lillian

--

Lillian T. Chong           
Associate Professor    
Department of Chemistry
University of Pittsburgh
219 Parkman Avenue
Pittsburgh, PA 15260
(412) 624-6026

[Sreyoshi Sur]

Hi,

I found another tutorial for OpenMM in the examples folder for WESTPA lib directory. The name of the directory is wca-dimer_openmm. If anyone else is also looking for it. This one uses the same method as used for NAMD and GROMACS packages. 

Thanks

Sreyoshi

[Lillian Chong]

Thanks a lot for pointing this out, Sreyoshi. We will mention this WCA dimer tutorial on the WESTPA tutorial page. Further details related to this tutorial can be found in the attached paper. 

Best,

Lillian