The residue name in our model is NGP(not glycine nor Proline), IGL(is Glycine) and IPR(is proline).
this is because the standard residue names(GLY, CYS for example) were already defined by openMM.
The openMM definition of standard residues demands the atoms in each residue match exactly with the real residue in nature.
But in our coarse grained model, we use 5 atom to represent each residues. so we have to create new names for them.
The output pdb file with residue name NGP, IGL, IPR can be converted to the standard pdb file with the following script
python ~/openawsem/helperFunctions/convertOpenmmTrajectoryToStandardMovie.py movie.pdb
If want to fixed the randomness in the simulation. you need to set the random seed in two places.
after the definition of integrator, add integrator.setRandomNumberSeed(A_NUMBER_AS_RANDOM_SEED)
change simulation.context.setVelocitiesToTemperature(Startkelvin) to simulation.context.setVelocitiesToTemperature(Startkelvin, A_NUMBER_AS_RANDOM_SEED)
For membrane protein simulation, you probably want first orient the protein relative to the membrane.