Hi all, I noticed that with the same system (4x4x4nm of water), same boost parameters (both E and alpha), that NAMD and OpenMM give different temperatures. Specifically, the AMDIntegrator results in a temp of about 325K, whereas NAMD stays at 300K. Adding an Andersen thermostat (since i wasn't sure ...

easy - cheers

Hi all, Is it possible to report or access the value of a subset of the potential energy function, dihedrals for example? I tried a couple of things - The PeriodicTorsionForce or CustomTorsionForce dont have a getPE (?) method, and the reporter functions only have total potentialEnergy. This value i...

Great, thanks Peter. Ill post back here with some code one day when it's finished.

Hi all, I'm interested in experimenting with metadynamics natively within OpenMM. There was a discussion about this ( https://github.com/pandegroup/openmm/issues/1796 ) that resulted in the CustomCVForce, but I haven't found an example to read through. If I understand this correctly, metadynamics ca...

Hi all, I have a pre-equilibrated cell, to which I added a ligand that dips over the edge of the cell, forming bad contacts with water. minimizeEnergy() is unable to remove the contacts - does this function work across the boundary? It can be fixed by increasing the z direction of the PBC (and recov...

cheers Peter!
Didn't know about the customcentroidbondforce. Ive implemented this and will watch and wait for explosions. Another possible restraint Ill try is a cylinder encompassing the interface, like k*(max(0, (x-x0)^2+(y-y0)^2-150)). Thanks!

Hi all, I'm hoping for some advice on how to implement some restraints. I have a protein with five-fold axial symmetry (ion channel with five subunits). I have a ligand that binds at the interface of two of any of the subunits. I'd like to have restraining walls that go through each subunit, restrai...

Looks like the last error is just because ChimeraX doesn't write CONECT records properly - leaves some atoms in a residue unbonded. Tested PyMol and it is the same, also the same with MDAnalysis which has a 'guess_bonds' function. But I guess the real issue is that CONECT records don't make sense wh...

OK so ChimeraX will write CONECT records if you just open and save again as pdb. But there are some other idiosyncrasies: - OpenMM won't load PDB's (using amber forcefield) with more than 99,999 atoms - after this, CHARMM-GUI writes '*****' as atom index, VMD includes letters, and OpenMM expects int...