def load_Coor(psfFile, coorFile): """ Load the binary coor file and extract coors. """ mol = Molecule() mol.load(psfFile, "parm7") mol.load(coorFile, "namdbin") allCoors = atomsel('all') xCor = allCoors.get('x') yCor = allCoors.get('y') zCor = allCoors.get('z') mol.delete() return xCor, yCor, zCor
def load_velocities(psfFile, velFile): """ Load the binary velocity file and extract velocities. """ mol = Molecule() mol.load(psfFile, "parm7") mol.load(velFile, "namdbin") allVelocities = atomsel('all') xVel = allVelocities.get('x') yVel = allVelocities.get('y') zVel = allVelocities.get('z') # conversion from binvel units to A/ps # convFactor = 20.4582651391 # xVel = [v * convFactor for v in xVel] # yVel = [v * convFactor for v in yVel] # zVel = [v * convFactor for v in zVel] mol.delete() return xVel, yVel, zVel