Alexander Matthew Payne

Hi @jchodera and @peastman, My temporary solution is to simply manually rename and renumber the part of the termini that correspond to the caps. Unfortunately CHARMM doesn't seem to have...

(this comment is for posterity) In discussion with @jchodera, we decided that since I'm using CHARMM param files to run these simulations, the behaviour of the forcefield is undefined if...

@charmm-gui As you can see from the discussion above, the way terminal caps are handled by CHARMM-GUI results in non-compliant PDB files, which results in less-than-ideal behaviour from OpenMM. Would...

The problem with the above comment is that such a compliant PDB file would likely not run with the correct forcefield behaviour with CHARMM, as the issue is caused by...

Thanks @peastman ! so something like this? ``` rmsd_cv = openmm.RMSDForce(positions, atom_indicies) energy_expression = f"(k/2)*max(0, RMSD-RMSDmax)^2" restraint_force = openmm.CustomCVForce(energy_expression) restraint_force.addCollectiveVariable('RMSD', rmsd_cv) restraint_force.addGlobalParameter('RMSDmax', 0.4) restraint_force.addGlobalParameter("k", 50) ``` And then to write...

This doesn't seem to be working for me. I've uploaded a jupyter notebook to play around with it. The simple "negative control" I'm trying to run is, if make this...

Ohhhh I can't read. My eyes just glazed over "groups (set={0,1,2,...,31})" in the documentation and for some reason assumed just that it meant that the integer input had to be...

I will close this if it behaves!

I will work on adding papers to our list to read, update the "dibbs" chart to reflect what I'm going to read, and help write the descriptions and collect the...

hi @Amireng72 , you gotta give more context than this or we will have to close this issue =P