Search found 1778 matches

by Peter Eastman
Mon Jun 17, 2019 11:10 am
Forum: OpenMM
Topic: CUDA 10 vs. CUDA 10.1
Replies: 3
Views: 55

Re: CUDA 10 vs. CUDA 10.1

If conda is listing an OpenMM package with "cuda92" in the name, that means you have that version of OpenMM installed. If you're trying to create your own build, you should first uninstall that one. Having two builds of OpenMM installed at once in the same conda environment will cause problems.
by Peter Eastman
Mon Jun 17, 2019 10:07 am
Forum: OpenMM
Topic: template residue error
Replies: 6
Views: 113

Re: template residue error

Your prm file has an error in it: CPH2 NG2R5C CPH1 HR3 3.0000 2 180.00 ! from HGR52 CG2R51 NG2R50 CG2R53 in CGenFF HR1 CPH2 NG2R5C CO6 0.0000 1 0.00 ! set to 0 to avoid overfitting HR1 CPH2 NG2R5C CPH1 2 180.00 ! from HGR52 CG2R53 NG2R50 CG2R51 in CGenFF CPH1 NG2R5C CO6 NCO6A 0.3720 4 0.00 ! from fi...
by Peter Eastman
Fri Jun 14, 2019 11:17 am
Forum: OpenMM
Topic: template residue error
Replies: 6
Views: 113

Re: template residue error

Could you post your files? I can take a look and see what's happening.
by Peter Eastman
Fri Jun 14, 2019 11:10 am
Forum: OpenMM
Topic: CUDA 10 vs. CUDA 10.1
Replies: 3
Views: 55

Re: CUDA 10 vs. CUDA 10.1

Currently we only have conda builds for versions up to 10.0. will the OpenMM executable name have to reflect the actual CUDA version (so that openmm_7.3.1_py_cuda92_rc_2 is wrong and should contain cuda10 or cuda101 in the name instead)? What executable are you talking about? You use OpenMM by impor...
by Peter Eastman
Wed Jun 12, 2019 1:00 pm
Forum: OpenMM
Topic: minimizeEnergy() reporter
Replies: 1
Views: 30

Re: minimizeEnergy() reporter

No, they're unrelated. Reporters apply when using the integrator to take steps. Energy minimization works very differently.
by Peter Eastman
Tue Jun 11, 2019 1:08 pm
Forum: OpenMM
Topic: AMOEBA FF for NPT, NVT
Replies: 3
Views: 63

Re: AMOEBA FF for NPT, NVT

Yes. Add a MonteCarloBarostat to your system. See http://docs.openmm.org/latest/userguide ... e-coupling.
by Peter Eastman
Mon Jun 10, 2019 8:39 am
Forum: OpenMM
Topic: template residue error
Replies: 6
Views: 113

Re: template residue error

Those files are in CHARMM format. Although they've been given the .txt extension, one is actually a .rtf file and the other is a .prm file. There are a couple of options. First, you could use ParmEd (https://github.com/ParmEd/ParmEd) to convert the files to an OpenMM force field file. You could then...
by Peter Eastman
Fri Jun 07, 2019 9:49 am
Forum: OpenMM
Topic: Hybrid implicit/explicit solvent simulation
Replies: 1
Views: 44

Re: Hybrid implicit/explicit solvent simulation

No, doing hybrid implicit/explicit solvent is hard. The problem is how to handle the interface between the two. If you just try to do what you described, you tend to get lots of strange boundary artifacts. Various approaches have been suggested for reducing them, but mostly people just stick to eith...
by Peter Eastman
Fri Jun 07, 2019 9:44 am
Forum: OpenMM
Topic: Particle-specific friction coefficient
Replies: 1
Views: 44

Re: Particle-specific friction coefficient

A similar question was asked recently in https://simtk.org/plugins/phpBB/viewtopicPhpbb.php?f=161&t=10404&p=0&start=0&view=&sid=848a20d9f8651e68f533c24db126d67f. That person wanted to vary the temperature between atoms rather than the friction coefficient, but the answer is basically the same. The b...
by Peter Eastman
Thu Jun 06, 2019 9:49 am
Forum: OpenMM
Topic: Setup PBC box
Replies: 2
Views: 66

Re: Setup PBC box

Topologies and Systems are different objects that represent different things. When you call forcefield.createSystem(topology, ...) to create a System from a Topology, that System has its default periodic box vectors set to the ones from the Topology. There's also a third place where box vectors get ...