Search found 21 matches

by Gideon Simpson
Thu May 30, 2019 10:31 am
Forum: OpenMM
Topic: Malloc error
Replies: 9
Views: 268

Re: Malloc error

I'm on MacOS 10.14.5 with an anaconda 2019.3 installation. OpenMM and associated libraries were freshly installed with conda install -c omnia openmm.
by Gideon Simpson
Thu May 30, 2019 9:07 am
Forum: OpenMM
Topic: Malloc error
Replies: 9
Views: 268

Malloc error

I've been playing with coulomb gases, and I got the following (mysterious) error when performing simulation.minimizeEnergy(): python(7187,0x1093785c0) malloc: *** error for object 0x7fe32d3871f8: pointer being freed was not allocated python(7187,0x1093785c0) malloc: *** set a breakpoint in malloc_er...
by Gideon Simpson
Thu May 23, 2019 7:09 am
Forum: OpenMM
Topic: Zeroing out Either Coulomb of LJ
Replies: 1
Views: 74

Zeroing out Either Coulomb of LJ

For a NonbondedForce, if I set the charge or the epsilon to zero on a particle, that obviously turns off either Coulomb or LJ forces on it. But does OpenMM then explicitly avoid calculating this term in the force? If not, is there a way to do that to speed up computations?
by Gideon Simpson
Wed May 22, 2019 5:46 am
Forum: OpenMM
Topic: CustomTorsionForce: How to obtain the dihedral angle?
Replies: 5
Views: 245

Re: CustomTorsionForce: How to obtain the dihedral angle?

Yes, this works: md_topology = mdtraj.Topology.from_openmm(simulation.topology) positions = state.getPositions().value_in_unit(unit.meter) traj = mdtraj.Trajectory([positions], md_topology) print('center of mass', mdtraj.compute_center_of_mass(traj)[0]) A few follow up questions: 1. Is there a way t...
by Gideon Simpson
Sat May 18, 2019 6:00 am
Forum: OpenMM
Topic: CustomTorsionForce: How to obtain the dihedral angle?
Replies: 5
Views: 245

Re: CustomTorsionForce: How to obtain the dihedral angle?

I had a similar question to this regarding the various functions that are a part of MDTraj, including dihedral angles. While it's clear to me how to calculate these quantities in a post-processing step, by dumping to disk and then loading in as an mdtraj Trajectory object, it's not at all clear how ...
by Gideon Simpson
Thu May 16, 2019 1:09 pm
Forum: OpenMM
Topic: New User Questions
Replies: 5
Views: 204

Re: New User Questions

Both suggestions work as expected. I'm guessing there's no straightforward way to modify the quenching tool (minimize energy) to restrict to 2D?
by Gideon Simpson
Wed May 15, 2019 7:13 pm
Forum: OpenMM
Topic: Periodic BCs and output issue
Replies: 5
Views: 146

Re: Periodic BCs and output issue

So does that mean that I'm writing PDB data incorrectly, or should I ask the Ovito people about how to post process it in the way I had anticipated?
by Gideon Simpson
Wed May 15, 2019 2:55 pm
Forum: OpenMM
Topic: Periodic BCs and output issue
Replies: 5
Views: 146

Re: Periodic BCs and output issue

I'm attaching a screen capture from Ovito. Again, this may be purely an artifact of how Ovito is interpreting the PDB output, in which case it's not really a problem. But notice that the dimensions of the cell, which started off cubic, are no longer uniform and that the locations of the particles ap...
by Gideon Simpson
Wed May 15, 2019 12:35 pm
Forum: OpenMM
Topic: Periodic BCs and output issue
Replies: 5
Views: 146

Periodic BCs and output issue

I am not sure if this is a genuine issue or not, but I ran some simple LJ cluster experiments with what I thought were periodic boundary conditions. The output, when viewed in Ovito, looks a bit more like shrink wrapped boundary conditions have been applied (i.e., the bounding box changes in size th...
by Gideon Simpson
Wed May 15, 2019 11:57 am
Forum: OpenMM
Topic: New User Questions
Replies: 5
Views: 204

Re: New User Questions

For a CustomIntegrator, is there a way to only manipulate particular degrees of freedom per particle? I see commands like addComputePerDof, but these appear to operate on the entire position, x, and entire velocity, v space. Is there a way to access x[0], x[1], etc.?