Search found 31 matches
- Mon Nov 18, 2019 3:52 am
- Forum: OpenMM
- Topic: Obtaining CustomNonbondedForce's shortest pairwise interaction
- Replies: 5
- Views: 1475
Re: Obtaining CustomNonbondedForce's shortest pairwise interaction
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...
- Fri Nov 15, 2019 7:18 am
- Forum: OpenMM
- Topic: Obtaining CustomNonbondedForce's shortest pairwise interaction
- Replies: 5
- Views: 1475
Re: Obtaining CustomNonbondedForce's shortest pairwise interaction
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...
- Wed Nov 13, 2019 5:07 am
- Forum: OpenMM
- Topic: Obtaining CustomNonbondedForce's shortest pairwise interaction
- Replies: 5
- Views: 1475
Obtaining CustomNonbondedForce's shortest pairwise interaction
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...
- Tue Jan 31, 2017 2:25 pm
- Forum: OpenMM
- Topic: OpenMM 7.1 Beta
- Replies: 7
- Views: 6117
Re: OpenMM 7.1 Beta
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...
- Tue Jan 10, 2017 8:13 am
- Forum: OpenMM
- Topic: CUDA PME with triclinic boxes using OpenMM 6.3.1
- Replies: 1
- Views: 467
CUDA PME with triclinic boxes using OpenMM 6.3.1
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
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
- Fri Mar 11, 2016 7:30 am
- Forum: OpenMM
- Topic: General debugging strategies for "ValueError: Energy is NaN"
- Replies: 2
- Views: 841
Re: General debugging strategies for "ValueError: Energy is
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...
- Wed Mar 09, 2016 7:15 am
- Forum: OpenMM
- Topic: General debugging strategies for "ValueError: Energy is NaN"
- Replies: 2
- Views: 841
General debugging strategies for "ValueError: Energy is NaN"
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...
- Wed Oct 14, 2015 5:38 am
- Forum: OpenMM
- Topic: PDBReporter options
- Replies: 5
- Views: 1091
Re: PDBReporter options
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 ...
- Sun Apr 19, 2015 5:51 am
- Forum: OpenMM
- Topic: Relative performance of various GPUs
- Replies: 22
- Views: 5019
Re: Relative performance of various GPUs
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
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
- Thu Apr 09, 2015 3:53 am
- Forum: OpenMM
- Topic: Relative performance of various GPUs
- Replies: 22
- Views: 5019
Re: Relative performance of various GPUs
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...