Hi Peter,

It is with version 7.1.1 installed via conda:
-Joe

Hello, I'd like to report an error I encounter when using the RPMDIntegrator in the latest version of OpenMM. When I call getState() on the RPMDIntegrator I receive the following error: Traceback (most recent call last): File "run-dynamics.py", line 135, in <module> state = simulation.integrator.get...

Hi Peter, Thanks for getting back to me. OPENMM_CUDA_COMPILER is set to /global/software/Core/CUDA/7.5.18/bin/nvcc I am running on Stanford's Xstream cluster, which I believe is configured with Nvidia Tesla K80 GPUs. As far as I can tell, I only have one copy of openmm on the system (installed via c...

Hello, I am puzzled by the following error I receive when testing my OpenMM installation: There are 4 Platforms available: 1 Reference - Successfully computed forces 2 CPU - Successfully computed forces 3 CUDA - Successfully computed forces Segmentation fault (core dumped) I installed the latest ver...

Hi Peter,

Can this be done within a Python script?

Thanks,
Joe

Ah, perfect, sorry I missed that. Thanks, Peter!

-Joe

Hello, I have come across the PLUMED plugin for OpenMM on the web and would like to use it in order to avoid Amber. Is there documentation somewhere for using the plugin?

Thank you!

Joe

Hi Peter,

I am able to do that currently to run a gas phase simulation or a simulation in implicit solvent, but would I be able to load the charmm files directly, solvate the molecule, and run the simulation in explicit water (using e.g. TIP4P)?

Thank you!
Joe

Hi, I would like to simulate a small molecule with explicit solvent in OpenMM. I have created CHARMM force field files using CGenFF: https://cgenff.paramchem.org/ . My question is whether it is possible to straightforwardly solvate this molecule and simulate it using an arbitrary explicit water mode...

Apologies, the website wouldn't allow me to attach my script and the structure pdb as well. Here is the python script. I can email the pdb file if you'd like to run it. Thank you, Joe run.py from __future__ import print_function from simtk.openmm import * from simtk.openmm.app import * from simtk.un...