Search found 1806 matches

by Peter Eastman
Fri Jul 19, 2019 2:37 am
Forum: OpenMM
Topic: Periodicity of Bond Forces
Replies: 6
Views: 64

Re: Periodicity of Bond Forces

That should be positions = simulation.context.getState(getPositions=True, enforcePeriodicBox=True).getPositions().value_in_unit(nanometer) You were missing the call to getPositions() on the State. What is not clear, how to set enforcePeriodicBox since I am not calling getState() directly. The last v...
by Peter Eastman
Wed Jul 17, 2019 7:57 am
Forum: OpenMM
Topic: Periodicity of Bond Forces
Replies: 6
Views: 64

Re: Periodicity of Bond Forces

Once again, there are two completely different issues here. It's important to understand what periodic boundary conditions mean and what effect they have. When you are simulating a periodic system, every "particle" really represents an infinite grid of particles repeating throughout space. Suppose y...
by Peter Eastman
Wed Jul 17, 2019 2:16 am
Forum: OpenMM
Topic: Updated Benchmark numbers?
Replies: 1
Views: 24

Re: Updated Benchmark numbers?

You can find benchmarks for 7.3 at https://simtk.org/plugins/moinmoin/openmm/Benchmarks. I've been trying to get the numbers at openmm.org updated for a while, but we've been having technical problems. Sorry about that!
by Peter Eastman
Wed Jul 17, 2019 2:13 am
Forum: OpenMM
Topic: What is the most recent supported version of CUDA to install for the next year or so?
Replies: 2
Views: 30

Re: What is the most recent supported version of CUDA to install for the next year or so?

Yes, 10.0 should be a fine version that will be supported for a long time. And yes, omnia/label/cuda100 is the right way to install it. See http://docs.openmm.org/latest/userguide ... ing-openmm.
by Peter Eastman
Wed Jul 17, 2019 2:10 am
Forum: OpenMM
Topic: Protein protein interactions
Replies: 1
Views: 24

Re: Protein protein interactions

That's an error coming from the server, not from OpenMM. It sounds like the PDB was having problems.
by Peter Eastman
Tue Jul 16, 2019 10:50 am
Forum: OpenMM
Topic: Periodicity of Bond Forces
Replies: 6
Views: 64

Re: Periodicity of Bond Forces

Periodic boundary conditions affect how forces are computed. You can still place particles at any position in space, but for purposes of computing the displacements between particles, it uses the shortest possible distance between all periodic pairs of the two particles. Independently of that, when ...
by Peter Eastman
Tue Jul 16, 2019 10:43 am
Forum: OpenMM
Topic: PBC question
Replies: 1
Views: 27

Re: PBC question

It depends on the details of what you're doing. PDB files only support storing a single set of periodic box vectors for the whole simulation. The PDBFile class therefore writes the ones stored in the Topology object. As long as that's correct, everything should be fine. But if you have a barostat in...
by Peter Eastman
Fri Jul 12, 2019 8:51 am
Forum: OpenMM
Topic: Compute distance map on GPU
Replies: 1
Views: 28

Re: Compute distance map on GPU

When you say, "on the CPU," what exactly does that mean? Is it written in Python? C++? How are you calculating it? Assuming you really want to do it on the GPU, there's no built in feature for that, so you'll need to write a plugin. The place to start is reading the developer guide: http://docs.open...
by Peter Eastman
Thu Jul 11, 2019 4:58 pm
Forum: OpenMM
Topic: Simple Binary Material
Replies: 9
Views: 114

Re: Simple Binary Material

Exponentiation is indicated with ^ not **. See http://docs.openmm.org/latest/userguide ... xpressions.
by Peter Eastman
Thu Jul 11, 2019 12:30 pm
Forum: OpenMM
Topic: Simulated tempering
Replies: 3
Views: 376

Re: Simulated tempering

Thanks! I'm glad it's working for you. The best way to cite OpenMM is to cite the first publication listed at https://simtk.org/plugins/publications/ ... blications (the 2017 one).