Bas Rustenburg
Bas Rustenburg
Could it also be made python 3 compatible?
It may also be helpful if it prints the help string if called without any arguments.
```py from __future__ import print_function from protons import app from simtk import unit, openmm as mm from protons.app import ConstantPHCalibration, ForceFieldProtonDrive, NCMCProtonDrive from protons.app import MetadataReporter, TitrationReporter, NCMCReporter, SAMSReporter import...
One of the things that will need to be paid attention to are the paths in the configuration of the documentation so that references to different classes work again. Additionally,...
Thanks for the feedback Peter and John! Very helpful suggestions. I'm familiar with variants, and that is how I plan to resolve this. I haven't gotten around to it yet....
/cbio/jclab/home/rustenburg/constph-grant/systems/simulations
Yes, but somehow all those log files have ended up in my home directory, instead of the qsub directory. They're called by the PDB file names, plus the usual `.o123456`...
Preliminary update on this: a decent amount of pdb files seem to have botched up loops, which may be the source for some of the simulation crashes that happened immediately...
@cxhernandez in the current setup, protons aren't removed from the topology, and the initial topology should have all possible protons included. During simulation, they're switched on and off by changing...
Tagging @jchodera .