FAQs

1. 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

2. 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)

3. For membrane protein simulation, you probably want first orient the protein relative to the membrane.

• https://opm.phar.umich.edu/ppm_server this server can help your achieve that.