Search found 16 matches

by Gideon Simpson
Sun Jun 23, 2019 12:50 pm
Forum: OpenMM
Topic: Simple Binary Material
Replies: 5
Views: 43

Re: Simple Binary Material

For a first problem, I want to study the solvated dimer problem from Example 1.3.2.4 of Lelievre, Rousset, and Stolz (if you have that book handy). In it, particles 1 and 2 interact through the pair potential V(r) = h * (1 - (r-r0-w)^2/w^2)^2, r = distance between particles 1 and 2, and h, r0, and w...
by Gideon Simpson
Fri Jun 21, 2019 1:22 pm
Forum: OpenMM
Topic: Simple Binary Material
Replies: 5
Views: 43

Re: Simple Binary Material

In principle, this is a non-bonded system, with different pair potentials depending on specifies. The simplest example i would like to do is a dimer in an LJ fluid. Here, Atoms 1 and 2 interact with each other via a bistable potential, and they interact with atoms 2,3,...,N via an LJ pair potential....
by Gideon Simpson
Fri Jun 21, 2019 12:44 pm
Forum: OpenMM
Topic: Simple Binary Material
Replies: 5
Views: 43

Simple Binary Material

I am interested in using OpenMM to simulate a simple binary material where I have three types of pair potentials for A-A, B-B, and A-B bonds. I've been looking at some of the documentation for this. Is the right approach here that I build an XML force file for this and a separate PDB file for the at...
by Gideon Simpson
Sat Jun 01, 2019 10:14 am
Forum: OpenMM
Topic: Malloc error
Replies: 9
Views: 178

Re: Malloc error

Yup, fixed it. Thanks.
by Gideon Simpson
Thu May 30, 2019 12:01 pm
Forum: OpenMM
Topic: Malloc error
Replies: 9
Views: 178

Re: Malloc error

Did a conda uninstall followed by a conda install -c omnia, which installed:

Code: Select all

The following NEW packages will be INSTALLED:

  openmm             omnia/osx-64::openmm-7.3.1-py37_cuda92_rc_2

Same results
by Gideon Simpson
Thu May 30, 2019 10:31 am
Forum: OpenMM
Topic: Malloc error
Replies: 9
Views: 178

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: 178

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: 50

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: 182

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: 182

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 ...