Thank you for the reply on this. Since you described this as docking, I assume you aren't really planning to do it with water, right? That is, you only have two molecules and your potential only depends on a single distance between them? Correct; the above was just a simple example. We plan to do th...

Thank you the reply on this. You want to calculate an interaction between two molecules by identifying the very closest distance between them, right? Given all atoms in molecule 1 and all atoms in molecule 2, you want to find the very closest pair. And then you want to compute a function of that dis...

Dear Forum, This question is cast within the context of using the rich OpenMM framework as a basic docking engine, in which there is only one class of force, CustomNonbondedForce, and making use of State.getPotentialEnergy() as a scoring metric. If one should set the following cutoff scheme with a C...

Hello, I've just been testing the RC via conda. I've found something with pdbfixer and I'm not sure if it is an issue with that package or the fact that it makes use of simtk.openmm.app.forcefield. Here's the code: #!/usr/bin/env python # # Installed via # conda create --name openmm python=2.7 # sou...

Dear OpenMM Devs,

Just a quick clarification. Given Fixed bug in PME with triclinic boxes #1487, I assume that one should be using OpenMM 7.0.1 and that OpenMM 6.3.1 still has this issue?

Many thanks,

Mark

Dear Peter, Thank you for these useful suggestions; the force grouping sounds great for localisation of the problem. I will take these on board for future. My problem turned out to be a bug in a customer file reporter that I had written. This was being used to write out a minimised structure, howeve...

Dear all, When observing non-deterministic "ValueError: Energy is NaN" from statedatareporter.py's _checkForErrors in standard simulations, are there any general strategies for debugging this? For instance, is there a way to increase the verbosity of _checkForErrors to localise the term that is caus...

This is snippet example of what Jason is referring to: import mdtraj.reporters ....<snip>... # Get the index of protein atoms only, # to enable omission of water and counter ions in the production trajectory traj = mdtraj.load('minimisation.pdb') top, bonds = traj.top.to_dataframe() protein_indices ...

Hi Peter,
Apologies for delay in response. The AMBER CUDA implementation does not support interpolation orders greater than 4, and OpenMM's order parameter seems not to be user definable. Hence this comparison cannot be made.

Thank you for the clarification.

Mark

size, spline order, alpha) are different is not a meaningful comparison. You need to adjust all of them at once to give optimal performance while maintaining the same level of accuracy. Agreed; hence, given the AMBER mdout file present, I assume the following would be correct? for i in range(system...