Search found 28 matches

by Istvan Kolossvary
Fri Jul 19, 2019 11:13 am
Forum: OpenMM
Topic: Periodicity of Bond Forces
Replies: 6
Views: 94

Re: Periodicity of Bond Forces

Thank you, Peter. I was wondering what the 5th return value of describeNextReport() was. It looks like, unknowingly, I was already writing out PBC coordinates. :)
by Istvan Kolossvary
Thu Jul 18, 2019 3:42 pm
Forum: OpenMM
Topic: Periodicity of Bond Forces
Replies: 6
Views: 94

Re: Periodicity of Bond Forces

I have a follow-up question regarding to call getState() with the enforcePeriodicBox argument. I have a simple reporter that writes out coordinates in (x,y,z) format (for some post processing) but I have a triclinic simulation cell and want to write out the coordinates enforcing PBC. The reporter lo...
by Istvan Kolossvary
Fri Feb 15, 2019 10:39 am
Forum: OpenMM
Topic: Restraints with reference position changing based on system dimension
Replies: 10
Views: 317

Re: Restraints with reference position changing based on system dimension

Thanks, Peter! I really appreciate your time, these small things are so difficult to figure out for mortals. :)
by Istvan Kolossvary
Fri Feb 15, 2019 8:31 am
Forum: OpenMM
Topic: Restraints with reference position changing based on system dimension
Replies: 10
Views: 317

Re: Restraints with reference position changing based on system dimension

Sorry, I am embarrassed to say but I don't know how to add a dummy atom.
by Istvan Kolossvary
Thu Feb 14, 2019 2:28 pm
Forum: OpenMM
Topic: Restraints with reference position changing based on system dimension
Replies: 10
Views: 317

Re: Restraints with reference position changing based on system dimension

Peter, it all sounds straightforward, but when I tried to define dummy atoms and adding the bonds I got lost. Could you show an example how to do what you are suggesting? I have about 100 CA atoms that I'd like to restrain, though, not just one.

Many thanks,

Istvan
by Istvan Kolossvary
Thu Feb 14, 2019 10:51 am
Forum: OpenMM
Topic: Dimer jumps with position restraints
Replies: 7
Views: 198

Re: Dimer jumps with position restraints

Just to go full circle, I tried the simulation NVT as well as NPT but both blow up the same way. Strictly speaking it is incorrect to use NPT with absolute restraining coordinates, but in practice resizing the simulation box has virtually no effect if weak restraints are sought. My system is a dimer...
by Istvan Kolossvary
Wed Feb 13, 2019 8:39 am
Forum: OpenMM
Topic: Dimer jumps with position restraints
Replies: 7
Views: 198

Re: Dimer jumps with position restraints

Did not make any difference, I am still getting large forces. I wonder, this may be a manifestation of https://github.com/pandegroup/openmm/issues/988, I'll try using zero atomic masses.
by Istvan Kolossvary
Tue Feb 12, 2019 9:49 am
Forum: OpenMM
Topic: Dimer jumps with position restraints
Replies: 7
Views: 198

Re: Dimer jumps with position restraints

I am rerunning the simulation applying explicit minimum distance convention to the restraints instead of using periodicdistance(). Will let you know if that makes a difference.
by Istvan Kolossvary
Tue Feb 12, 2019 8:50 am
Forum: OpenMM
Topic: Dimer jumps with position restraints
Replies: 7
Views: 198

Re: Dimer jumps with position restraints

This is NOT the reporter/visualization issue that can be fixed as you suggest. The problem is that restrained atoms jump periodic boxes and huge forces arise, even though using periodicdistance().
by Istvan Kolossvary
Mon Feb 11, 2019 4:44 pm
Forum: OpenMM
Topic: Dimer jumps with position restraints
Replies: 7
Views: 198

Dimer jumps with position restraints

Hi, I have encountered something really puzzling. I simulate a dimer and I apply weak position restraints on about two thirds of the CA atoms in both monomers. If it wasn't for the position restraints I would of course expect the monomers to jump back and forth between neighboring periodic cells bre...