help='Number of thread-MPI threads to start, default=0',
type=float,
default=0)
parser.add_argument('-gpu_id',
action="store",
dest="gpuid",
help='List of GPU device id-s to use, default=\"\" ',
default="None")
return parser
if __name__ == "__main__":
my_parser = parser_input()
args = my_parser.parse_args()
dt = args.dt
nsteps = 1000 * args.time / dt
sys_prod = gmx.GmxSys()
sys_prod.nt = args.nt
sys_prod.ntmpi = args.ntmpi
if args.gpuid != "None":
sys_prod.gpu_id = args.gpuid
sys_prod.extend_equi_prod(args.tpr, nsteps=nsteps)
print("\n\nProduction extension was sucessfull ")
sys_prod.display()
parser = argparse.ArgumentParser(description="Create the topologie file\
from a structure pdb file")
parser.add_argument('-f', action="store", dest="f",
help='Input PDB file', type=str, required=True)
parser.add_argument('-o', action="store", dest="o",
help='Output directory', type=str, required=True)
parser.add_argument('-vsite', action="store_true", dest="vsite_flag",
help='Use virtual site for hydrogens')
return parser
if __name__ == "__main__":
my_parser = parser_input()
args = my_parser.parse_args()
if args.vsite_flag:
vsite = "hydrogens"
else:
vsite = "none"
sys_name = args.f.split("/")[-1][:-4]
md_sys = gmx.GmxSys(name=sys_name, coor_file=args.f)
md_sys.prepare_top(out_folder=args.o, vsite=vsite)
md_sys.create_box(dist=1.0, box_type="dodecahedron", check_file_out=True)
print("\n\nTopologie creation was sucessfull \n\tTopologie directorie :\t" + args.o)
md_sys.display()
do a minimisation and a vacuum equilibration")
parser.add_argument('-seq', action="store", dest="seq",
help='Peptide sequence', type=str, required=True)
parser.add_argument('-o', action="store", dest="o",
help='Output Directory', type=str, required=True)
parser.add_argument('-m_steps', action="store", dest="min_steps",
help='Minimisation nsteps, default=1000', type=int, default=1000)
parser.add_argument('-time', action="store", dest="time",
help='Vacuum equilibration time(ns), default = 1ns', type=float, default=1)
return parser
if __name__ == "__main__":
my_parser = parser_input()
args = my_parser.parse_args()
dt = 0.001
step = 1000 * args.time / dt
sequence = args.seq
out_folder = args.o
em_nsteps = args.min_steps
peptide = gmx.GmxSys(name='pep_' + sequence)
peptide.create_peptide(sequence=sequence, out_folder=out_folder,
em_nsteps=em_nsteps, equi_nsteps=step)
print("\n\nPeptide Creation was sucessfull \n\tPeptide directorie :\t" + args.o)
peptide.display()
type=float,
default=0)
parser.add_argument('-gpu_id',
action="store",
dest="gpuid",
help='List of GPU device id-s to use, default=\"\" ',
default="None")
return parser
if __name__ == "__main__":
my_parser = parser_input()
args = my_parser.parse_args()
sys_min = gmx.GmxSys(name=args.name, coor_file=args.f, top_file=args.p)
sys_min.nt = args.nt
sys_min.ntmpi = args.ntmpi
if args.gpuid != "None":
sys_min.gpu_id = args.gpuid
sys_min.em_2_steps(out_folder=args.o,
name=args.name,
no_constr_nsteps=args.min_steps,
constr_nsteps=args.min_steps,
posres="",
create_box_flag=args.box)
sys_min.convert_trj(traj=False)
print("\n\nMinimisation was sucessfull \n\tMinimzed directory :\t" +
args.o)
args = parser.parse_args()
# General args:
dt = args.dt
out_folder = args.o
sys_name = args.name
maxwarn = args.maxwarn
# Peptide args:
sequence = args.seq
em_nsteps = args.em_steps
pep_step = 1000 * args.pep_time / dt
# Create peptide:
peptide = gmx.GmxSys(name='pep_' + sequence)
peptide.nt = args.nt
peptide.ntmpi = args.ntmpi
if args.gpuid != "None":
peptide.gpu_id = args.gpuid
peptide.create_peptide(sequence=sequence, out_folder=out_folder + "/" + sequence,
em_nsteps=em_nsteps, equi_nsteps=pep_step, posre_post="_pep")
peptide.display()
# Starting system args:
coor_sys = args.f_sys
top_sys = args.p_sys
pep_num = args.num_mol
# Insert peptide:
help='Output Directory')
parser.add_argument('-n',
action="store",
dest="name",
help='Output file name')
return parser
if __name__ == "__main__":
my_parser = parser_input()
args = my_parser.parse_args()
sys_raw = gmx.GmxSys(name=args.name,
coor_file=args.f_sys,
top_file=args.p_sys)
mol_gmx = gmx.GmxSys(name="mol", coor_file=args.f_mol, top_file=args.p_mol)
sys_raw.display()
mol_gmx.display()
sys_raw.insert_mol_sys(mol_gromacs=mol_gmx,
mol_num=args.num_mol,
new_name=args.name,
out_folder=args.o,
check_file_out=True)
print("\n\nInsertion was sucessfull \n\tSystem directory :\t" + args.o +
"\n\tsystem coor file:\t" + sys_raw.coor_file +
"\n\tsystem top file:\t" + sys_raw.top_file)
parser.add_argument('-ntmpi', action="store", dest="ntmpi",
help='Number of thread-MPI threads to start, default=0',
type=float, default=0)
parser.add_argument('-gpu_id', action="store", dest="gpuid",
help='List of GPU device id-s to use, default=\"\" ', default="None")
return parser
if __name__ == "__main__":
my_parser = parser_input()
args = my_parser.parse_args()
vsite = "none"
peptide = gmx.GmxSys(name=args.name, coor_file=args.f)
peptide.nt = args.nt
peptide.ntmpi = args.ntmpi
if args.gpuid != "None":
peptide.gpu_id = args.gpuid
if args.cyclic_flag:
peptide.cyclic_peptide_top(out_folder=args.out_dir + '/top')
else:
peptide.add_top(out_folder=args.out_dir + '/top',
pdb2gmx_option_dict={'vsite': 'no', 'ignh': 'yes', 'ter': 'no'})
peptide.em(out_folder=args.out_dir + '/em', name="min_" + args.name,
nsteps=args.min_steps, posres="", nstxout=1000, create_box_flag=True,
constraints="none")
maxwarn = args.maxwarn
min_steps = args.min_steps
dt_HA = args.dt_HA
dt = args.dt
HA_step = 1000 * args.HA_time / dt_HA
CA_step = 1000 * args.CA_time / dt
CA_LOW_step = 1000 * args.CA_LOW_time / dt
prot_top_folder = args.o + "/top_prot/"
prot_min_folder = args.o + "/em_prot/"
sys_top_folder = args.o + "/top_sys/"
sys_em_equi_folder = args.o + "/em_equi_sys/"
if args.p != "None":
prot_sys = gmx.GmxSys(name=sys_name, coor_file=args.f, top_file=args.p)
else:
prot_sys = gmx.GmxSys(name=sys_name, coor_file=args.f)
prot_sys.nt = args.nt
prot_sys.ntmpi = args.ntmpi
if args.gpuid != "None":
prot_sys.gpu_id = args.gpuid
if args.p == "None":
prot_sys.prepare_top(out_folder=prot_top_folder, vsite=vsite)
prot_sys.create_box(dist=1.0, box_type="dodecahedron", check_file_out=True)
prot_sys.em_2_steps(out_folder=prot_min_folder,
name=sys_name,
no_constr_nsteps=min_steps,