How embarrassing!!!
Thank you, Peter!!

An add-on: This error seems related to the use of set.Parameter() in the context of a Simulation object. The following works just fine: # Build system system = psf.createSystem(params, nonbondedMethod=inputs.coulomb, nonbondedCutoff=inputs.r_off*nanometers, constraints=inputs.cons, ewaldErrorToleran...

Hi, all, I am experiencing a problem with OpenMM, version -7.4.2-py37_cuda101_rc1. I tested the platforms CPU and CUDA, both have the same issue: I want to update a global parameter with context.setParamter() which fails with the following error: Traceback (most recent call last): File "openmm_run.p...

Thanks, Peter, that was very helpful!
Best,
Martin

Hi everybody, I would have a question regarding OpenMM's implementation of the implicit solvation model GBn2. Are there any terms for the nonpolar solvation (proportional to the SASA)? In their article preseneting GBn2 [ J. Chem. Theory Comput., 2013, 9 (4), pp 2020–2034; DOI: 10.1021/ct3010485 ] Ca...

Hi, Peter,
OK, this is clear now!
Thanks for the speedy reply,
Martin

Hi, Peter, If I understand your post correctly, using amber99_obc.xml (with forcefield object) and the argument implicitSolvent=OBC2 (with AmberPrmtopFile) should give the same solvation model. In the User Guid documentation of OpenMM 6.2, it says, however, that *_obc.xml uses specialized GBSA-Param...

Hi, Lee-Ping,

Yes, indeed, the proprties wer4e not added in the Simulation object, how embarrassing!
It's now working fine.

Best,
Martin

Hi, Peter, Thanks for your response! Please find below the information you asked for. Best, Martin Here is the Python code (it is based on the test case simulateAmber.py): *** from simtk.openmm.app import * from simtk.openmm import * from simtk.unit import * from sys import stdout platform = Platfor...

Hi, Peter,

I have actually the same problem; I have two GPU cards but whatever I specify with

properties = {'CudaDeviceIndex': 'X'}

with X=0,1

has no impact on which GPU card OpenMM is executed; it's always the first card ('0').

Best,
Martin