def energy_minimize(): gen_mdp('EM') utils.update("energy_minimize", "running gmx grompp and mdrun for energy minimization...") os.system( "gmx grompp -f EM.mdp -c {0} -p topol.top -o EM.tpr -r {0} >> builder.log 2>&1" .format(universe.get('d_nameList')[-1])) os.system("gmx mdrun -deffnm EM -c EM.pdb >> builder.log 2>&1") utils.add_to_nameList("EM.pdb")
def energy_pcouple(): gen_mdp('NPT') utils.update("energy_pcouple", "running gmx grompp and mdrun for pressure coupling...") os.system( "gmx grompp -f NPT.mdp -c {0} -p topol.top -o NPT.tpr -r {0} >> builder.log 2>&1" .format(universe.get('d_nameList')[-1])) os.system("gmx mdrun -deffnm NPT -c NPT.pdb >> builder.log 2>&1") utils.add_to_nameList("NPT.pdb")
def energy_tcouple(): gen_mdp('NVT') utils.update("energy_tcouple", "running gmx grompp and mdrun for temperature coupling...") os.system( "gmx grompp -f NVT.mdp -c {0} -p topol.top -o NVT.tpr -r {0} >> builder.log 2>&1" .format(universe.get('d_nameList')[-1])) os.system( "gmx mdrun -deffnm NVT -c {0}_NVT.pdb >> builder.log 2>&1".format( universe.get('d_pdbName'))) utils.add_to_nameList("{0}_NVT.pdb".format(universe.get('d_pdbName')))