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...

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....

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...

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 ...

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 ...

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...

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

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...

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...

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...