Search found 1889 matches

by Peter Eastman
Fri Sep 13, 2019 1:31 pm
Forum: OpenMM
Topic: (POSSIBLE BUG): GBn and GBn2 exhibit unexpected behaviors unlike HCT, OBC1, OBC2 in openmm and igb=8 in amber 18
Replies: 7
Views: 105

Re: (POSSIBLE BUG): GBn and GBn2 exhibit unexpected behaviors unlike HCT, OBC1, OBC2 in openmm and igb=8 in amber 18

Is there any way to force a GB parameter set for each atom? Yes, it's very similar to the code above but call setParticleParameters() to give it the new parameters to use for each particle. You need to do that before you create the context/simulation. After you create it, it will ignore any further...
by Peter Eastman
Fri Sep 13, 2019 12:56 pm
Forum: OpenMM
Topic: AMOEBA03 water structure reproduction
Replies: 6
Views: 83

Re: AMOEBA03 water structure reproduction

I see another problem in your script: you shouldn't call createStandardBonds(). There's almost never a reason to do that yourself. PDBFile does it automatically when a file is loaded. By calling it again, you created a second set of bonds for every molecule, which effectively means all the force con...
by Peter Eastman
Fri Sep 13, 2019 12:31 pm
Forum: OpenMM
Topic: pdb file does not open in openmm
Replies: 14
Views: 246

Re: pdb file does not open in openmm

Yes. You can upgrade with the command

Code: Select all

conda update -c omnia openmm-setup
by Peter Eastman
Fri Sep 13, 2019 10:19 am
Forum: OpenMM
Topic: AMOEBA03 water structure reproduction
Replies: 6
Views: 83

Re: AMOEBA03 water structure reproduction

You also need the argument rigidWater=False in the call to createSystem(). If rigidWater=True (the default), water molecules are rigid regardless of the value of the constraints argument. That's because most standard water models are defined to be rigid, so you need that even if you don't want any c...
by Peter Eastman
Thu Sep 12, 2019 4:47 pm
Forum: OpenMM
Topic: Changelog for versions
Replies: 3
Views: 29

Re: Changelog for versions

There's lots more detail at https://github.com/openmm/openmm/releases/tag/7.4.0. If you want even more detail than that, you can of course view the full list of merged pull requests, but I assume that's more detail than you want. :)
by Peter Eastman
Thu Sep 12, 2019 3:11 pm
Forum: OpenMM
Topic: AMOEBA03 water structure reproduction
Replies: 6
Views: 83

Re: AMOEBA03 water structure reproduction

It should exactly reproduce the literature value. Can you post the code you're using?

Did you remember to set rigidWater=False? AMOEBA water is supposed to be flexible.
by Peter Eastman
Thu Sep 12, 2019 12:48 pm
Forum: OpenMM
Topic: (POSSIBLE BUG): GBn and GBn2 exhibit unexpected behaviors unlike HCT, OBC1, OBC2 in openmm and igb=8 in amber 18
Replies: 7
Views: 105

Re: (POSSIBLE BUG): GBn and GBn2 exhibit unexpected behaviors unlike HCT, OBC1, OBC2 in openmm and igb=8 in amber 18

You can retrieve a list of the force on every atom like this: forces = simulation.context.getState(getForces=True).getForces() GBn and GBn2 both get implemented with CustomGBForce. To look up the particle parameters, you first look up the force, then loop over all the particles and print out the par...
by Peter Eastman
Thu Sep 12, 2019 11:19 am
Forum: OpenMM
Topic: (POSSIBLE BUG): GBn and GBn2 exhibit unexpected behaviors unlike HCT, OBC1, OBC2 in openmm and igb=8 in amber 18
Replies: 7
Views: 105

Re: (POSSIBLE BUG): GBn and GBn2 exhibit unexpected behaviors unlike HCT, OBC1, OBC2 in openmm and igb=8 in amber 18

That does sound strange. The first thing I would try is loading up a single conformation in both Amber and OpenMM and writing out the force on every atom. How well do they agree? If there are significant differences, the next thing would be to write out the GB parameters for every atom and see if an...
by Peter Eastman
Wed Sep 11, 2019 12:44 pm
Forum: OpenMM
Topic: RPMD_Energies
Replies: 21
Views: 362

Re: RPMD_Energies

No idea then. If you can provide a complete self-contained test case, I'll take a look and see where the difference is coming from. I suspect some calculation somewhere must be getting done in single precision. The relative difference between the values is about 2e-5, which is right around what you'...