Search found 1755 matches

by Peter Eastman
Mon May 20, 2019 4:15 pm
Forum: OpenMM
Topic: Nucleic acid Tinker 2018 parameters to xml conversion
Replies: 2
Views: 52

Re: Nucleic acid Tinker 2018 parameters to xml conversion

We haven't yet converted the nucleotide parameters to OpenMM format. Thanks for pointing that out. We really ought to. The conversion of AMOEBA was originally done with the script at https://github.com/pandegroup/openmm/blob/master/devtools/forcefield-scripts/processTinkerForceField.py. In principle...
by Peter Eastman
Sat May 18, 2019 2:30 pm
Forum: OpenMM
Topic: CustomTorsionForce: How to obtain the dihedral angle?
Replies: 3
Views: 106

Re: CustomTorsionForce: How to obtain the dihedral angle?

The following code might have some errors in it, but it should give you the idea. First, you'll need a MDTraj Topology object: topology = mdtraj.from_openmm(simulation.topology) Now query the current positions from OpenMM and create a Trajectory from them. state = simulation.context.getState(getPosi...
by Peter Eastman
Sat May 18, 2019 2:16 pm
Forum: OpenMM
Topic: problem with Installation of OpenMM 7.3.1 with Cuda 9.2 and 10.0 for heterogeneous cluster
Replies: 2
Views: 26

Re: problem with Installation of OpenMM 7.3.1 with Cuda 9.2 and 10.0 for heterogeneous cluster

CUDA 9.2 doesn't support Turing GPUs. It was released before they came out. In addition to needing the runtime libraries, it also needs the nvcc compiler, which by default it expects to be at /usr/local/cuda/bin/nvcc. In your case, that's the CUDA 9.2 version, which doesn't support your GPU. You can...
by Peter Eastman
Thu May 16, 2019 1:13 pm
Forum: OpenMM
Topic: New User Questions
Replies: 5
Views: 79

Re: New User Questions

If your initial coordinates are confined to the xy plane, and all forces are in that plane, then the minimizer shouldn't ever move the particles out of it. But if you do have forces acting out of the plane, there's no way to prevent the minimizer from responding to them. The best you could do is add...
by Peter Eastman
Thu May 16, 2019 8:22 am
Forum: OpenMM
Topic: Periodic BCs and output issue
Replies: 5
Views: 46

Re: Periodic BCs and output issue

Neither one. It just means you should ignore the box it's drawing around the atoms. It doesn't mean what you think it does.
by Peter Eastman
Wed May 15, 2019 4:54 pm
Forum: OpenMM
Topic: Periodic BCs and output issue
Replies: 5
Views: 46

Re: Periodic BCs and output issue

That looks to me like the box it's drawing is the minimum box containing all the particles. Which is not the same as the periodic box used in the simulation.
by Peter Eastman
Wed May 15, 2019 2:34 pm
Forum: OpenMM
Topic: Periodic BCs and output issue
Replies: 5
Views: 46

Re: Periodic BCs and output issue

I'm not sure what you mean by shrink wrapped boundary conditions. Does your simulation include a barostat? If so, the box will change size. Otherwise, it should stay fixed. Since you specified enforcePeriodicBox=True, the output should have all molecules translated into a single box. That is applied...
by Peter Eastman
Wed May 15, 2019 2:29 pm
Forum: OpenMM
Topic: New User Questions
Replies: 5
Views: 79

Re: New User Questions

One easy way is like this: integrator.addComputePerDof("x", "vector(_x(x), _y(x), 0)") That will set the z component of the position to 0. Another way is to create a per-DOF variable, and set it to (1, 1, 0) for each particle. Then you can multiply any calculation by that variable, and the z compone...
by Peter Eastman
Tue May 14, 2019 11:33 am
Forum: OpenMM
Topic: New User Questions
Replies: 5
Views: 79

Re: New User Questions

Is it absolutely necessary to specify an integrator to do anything? Anything that requires a Context, yes. If you're just doing static energy evaluations, it doesn't matter what integrator you use. What is the role of the topology data structure? You need it for any of the following: using Modeller...
by Peter Eastman
Mon May 13, 2019 9:06 am
Forum: OpenMM
Topic: Increase temperature of specific atoms
Replies: 1
Views: 22

Re: Increase temperature of specific atoms

Interesting question. The built in integrators/thermostats apply the same temperature to the whole system. They don't have an option to use different temperatures for different atoms. But you could create a CustomIntegrator that does that. You could use one of the integrators from https://github.com...