Search found 27 matches
- Tue Jun 12, 2018 1:13 am
- Forum: OpenMM
- Topic: Fixed atoms (mass=0) are moving with pressure coupling
- Replies: 1
- Views: 102
Re: Fixed atoms (mass=0) are moving with pressure coupling
I just checked the source and it looks like the current implementation does scale COM as oppose to the individual atoms. But the problem for my case was that I do not use any bonds for the metal oxide since I'm fixing it in space, and context.getMolecules(); does not parse this residue as a molecule...
- Tue Jun 12, 2018 12:55 am
- Forum: OpenMM
- Topic: Fixed atoms (mass=0) are moving with pressure coupling
- Replies: 1
- Views: 102
Fixed atoms (mass=0) are moving with pressure coupling
Hi all, I recently encountered this problem of using pressure coupling with position restraints for some of the atoms. It looks like both the MonteCarloAnisotropicBarostat and MonteCarloMembraneBarostat are scaling the positions of all the particles, even the particles fixed in position with mass=0....
- Tue Mar 07, 2017 12:35 pm
- Forum: OpenMM
- Topic: Rigid molecule with multiple correlated constraints
- Replies: 6
- Views: 245
Re: Rigid molecule with multiple correlated constraints
Thanks for the explanation. Yes I thought it might not satisfy the dof in 2D, and it makes sense now. I'll probably play around with different strengths of impropers and/or some bond constraints without dummy particles (ex, constraining O-O bond lengths and putting non-constrained bonds for the inte...
- Tue Mar 07, 2017 11:04 am
- Forum: OpenMM
- Topic: Rigid molecule with multiple correlated constraints
- Replies: 6
- Views: 245
Re: Rigid molecule with multiple correlated constraints
Another issue with adding a dummy particle for the out of plane constraint is that one cannot assign constraints for massless particles. So if I do the constraints in this way, I have to set a small mass for the dummy particle which is a bit strange and deviates from the actual mass distribution of ...
- Tue Mar 07, 2017 10:01 am
- Forum: OpenMM
- Topic: Rigid molecule with multiple correlated constraints
- Replies: 6
- Views: 245
Re: Rigid molecule with multiple correlated constraints
Thank you for the suggestion of adding dummy particle out of plane. I agree that it's more robust way of constraining planar molecule. Although I still don't understand why the applying constraints to velocities would not assign a value even during initialization. In practice, constrained distances ...
- Mon Mar 06, 2017 9:30 pm
- Forum: OpenMM
- Topic: Rigid molecule with multiple correlated constraints
- Replies: 6
- Views: 245
Rigid molecule with multiple correlated constraints
Is it possible to use constraints to fix a molecule completely rigid and planar? I'm testing a polarizable nitrate force field (NO3-) for certain ionic liquids. For non-polarizable ones I can get away with putting some improper dihedrals, but the polarizable FF was pulling the dihedral always too st...
- Mon Mar 06, 2017 9:17 pm
- Forum: OpenMM
- Topic: Anisotropic pressure coupling with hexagonal box?
- Replies: 4
- Views: 187
Re: Anisotropic pressure coupling with hexagonal box?
Peter,
Updating Openmm to 7.1 fixed the problem, and the simulation is now running fine up to several tens of ns. (The simulation is still running.)
Thanks for the help ! (But I'm going to bug you with another question ...
)
ChangYun
Updating Openmm to 7.1 fixed the problem, and the simulation is now running fine up to several tens of ns. (The simulation is still running.)
Thanks for the help ! (But I'm going to bug you with another question ...
![Laughing :lol:](./images/smilies/icon_lol.gif)
ChangYun
- Wed Mar 01, 2017 6:57 pm
- Forum: OpenMM
- Topic: Anisotropic pressure coupling with hexagonal box?
- Replies: 4
- Views: 187
Re: Anisotropic pressure coupling with hexagonal box?
The system blows up and the energy rapidly increases to reach the NaN. The error msg is weird though, since I initially got the usual 'energy value is NaN' error, which is typical for the system that's blowing up, but I tried one last time today and got 'the periodic box size has decreased to less t...
- Fri Feb 24, 2017 12:41 am
- Forum: OpenMM
- Topic: Anisotropic pressure coupling with hexagonal box?
- Replies: 4
- Views: 187
Anisotropic pressure coupling with hexagonal box?
Hi all, Is it possible to simulate a system with triclinic box with an semi-isotropic pressure coupling such as membrane barostat? I particularly want to simulate a hexagonal box with unknown box dimensions to run a self-assembly simulation of hexagonal phase. I tried to use the membrane barostat. T...
- Thu Jul 14, 2016 1:57 pm
- Forum: OpenMM
- Topic: PBC and translation of molecules in openmm-dcdreporter
- Replies: 3
- Views: 159
Re: PBC and translation of molecules in openmm-dcdreporter
Thank you for clarifying it. Does the reporters update the positions of the simulation.context too? I'm curious if I can use unwrapped positions during the simulation, while using the reporters to record the wrapped positions. If the reporters are updating the positions of the simulation object, I m...