Search found 21 matches

by Gideon Simpson
Wed Jul 17, 2019 6:56 am
Forum: OpenMM
Topic: Periodicity of Bond Forces
Replies: 6
Views: 100

Re: Periodicity of Bond Forces

I'm still a bit concerned about this. Consider the following two figures for my problem with a dimer joined by a CustomBondForce and the rest interacting through a nonbonded force. In both figures, there is the one blue atom outside of the periodic domain [0,10]X[0,10]. I would expect this atom to b...
by Gideon Simpson
Tue Jul 16, 2019 7:43 am
Forum: OpenMM
Topic: Periodicity of Bond Forces
Replies: 6
Views: 100

Periodicity of Bond Forces

I've been playing with a CustomBondForce, and I've noticed that the pairs of atoms can drift outside of the periodic box, despite calling setUsesPeriodicBoundaryConditions(True). On the the other hand, the center of the bonds remains in the periodic domain. Is this the expected behavior? Is there a ...
by Gideon Simpson
Sun Jul 14, 2019 8:00 pm
Forum: OpenMM
Topic: Simple Binary Material
Replies: 9
Views: 156

Re: Simple Binary Material

I'm seeing some slightly unexpected behavior when using a CustomBondForce to represent the interaction of the two atoms making up the dimer. I'm trying to run on a periodic domain, but I see the two dimer atoms drifting out of the periodic box. I've tried using setUsesPeriodicBoundaryConditions(True)
by Gideon Simpson
Thu Jul 11, 2019 6:09 pm
Forum: OpenMM
Topic: Simple Binary Material
Replies: 9
Views: 156

Re: Simple Binary Material

Yup, that did it.
by Gideon Simpson
Thu Jul 11, 2019 4:53 pm
Forum: OpenMM
Topic: Simple Binary Material
Replies: 9
Views: 156

Re: Simple Binary Material

I'm having some difficulty with the dimer model problem. I attempted to use the commands: # remove NonbondedForce interaction between 0 and 1 force.addException(0, 1, 0.0*charge*charge, sigma, 0.0*epsilon) system.addForce(force) # add custom force between 0 and 1 (simple version, for now) dimer_forc...
by Gideon Simpson
Sun Jun 23, 2019 12:50 pm
Forum: OpenMM
Topic: Simple Binary Material
Replies: 9
Views: 156

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: 9
Views: 156

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: 9
Views: 156

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: 253

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: 253

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

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