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')))