Many thanks, that makes sense. I initially used to have those lines in
get_pcoord.sh, but I had to make a few changes:
1) In the openMM script (common_files/run_md.py) which runs the segments, I'm reading the bstate.pdb straight from common_files/bstate.pdb, so I don't need to copy it in every folder. This is how I read them in the MD simulator:
pdb = PDBFile('../../../common_files/bstate.pdb')
psf = CharmmPsfFile('../../../common_files/bstate.psf')
2) For basis.xml, how and where is that generated? Because when I switched from NaCl to my protein system, it used to give me an error that the number of atoms didn't match. So I now just generate it myself and copy it to the bstates/01 (I renamed it seg.xml). See the following excepts from get_pcoord.sh
cp $WEST_SIM_ROOT/common_files/bstate.psf bstate.psf
cp $WEST_SIM_ROOT/common_files/bstate.xml seg.xml
cp $WEST_SIM_ROOT/common_files/bstate.dcd seg.dcd
3) I had to change the topology from .xml to .psf, as I'm using a CHARMM force field. I'm using .xml just to save/resume the state of the simulation in openMM.
What are my solutions in this case?
Razvan