That makes more sense - thanks!

I'd like to create a pure membrane and water system. My first approach went like this: modeller = app.Modeller(Topology(), Quantity([], nanometer)) modeller.addMembrane(omm_forcefield, 'POPC') but this raises an error at this line of Modeller: 1296 proteinMinPos = Vec3(*[min((p[i] for p in proteinPo...

Thanks Peter - success. Ill check that page first in future :')

Hi, So this time I'm looking to remove the native PeriodicTorsionForce and replace it with a CustomTorsionForce (same reason - for tempering the force). Implementing it seemed easy and I got accurate potential energy when I compared alanine dipeptide with and without the replacement force. But metad...

Thanks Peter, that explains the modifications I saw for PME.

Hi all, I'd like to do serial solute tempering by scaling nonbonded interactions between a solute and the surroundings - similar to what is done for alchemical transformations in the tutorial at: http://openmm.org/tutorials/alchemical-free-energy/ The equation given for the CustomNonbondedForce ther...

OK, solution that should persist if they change CUDA/python version. You have to reset the runtime after installing to recognise installed packages. Full sequence is: !wget https://repo.continuum.io/miniconda/Miniconda3-4.5.4-Linux-x86_64.sh && bash Miniconda3-4.5.4-Linux-x86_64.sh -bfp /usr/local !...

Managed to get around the python version issue by specifying the a python3.6 build explicitly: !time conda install -y -q -c conda-forge -c omnia/label/cuda101 -c omnia openmm=7.4.1=py36_cuda101_rc_1 This appears to install correctly, and the simtk package is present in the right directory. However a...

Hi all, Sorry, not an OpenMM question directly. Has anyone had consistent success running OpenMM in a colab instance? I've maxed out all my GPUs but of course still want to work on other scripts! The most recent success I've seen is at: https://github.com/molmod/openmm-tutorial-msbs/blob/master/setu...

Spot on, thanks so much Peter. Ultimately my error was that I normally add pairwise interaction groups to the CustomNonbondedForce to implement a short-range repulsive potential that prevents aggregation of drugs. Anyway while trying to get a minimal example I reduced the number of drugs to 1, meani...