def pump_at_res(self,res_ids,mode=0,frequency=1,force=100,time=500,velocity=False,temperature=300,cuda='0',ratio_threshold=2,top=5,window=1,rm_file=True,bb=False):
'''
Run pumped md and return the pumped residues if index>0
'''
pdb_file = self.pdb
if isinstance(res_ids,int):
res_index = str(res_ids)
if isinstance(res_ids,list):
res_index = str()
for temp_id in res_ids:
res_index = res_index+str(temp_id)+'_'
if self.index==0:
self.index+=1
atom_ids = utils.get_atom_ids(pdb_file,res_ids)
vec = self.calc_nm_vec(res_ids,mode)
plumed_in = self.write_plumed_file(atom_ids,vec,frequency=frequency,force=force,res_index=res_index)
in_file = self.write_prod_input_file(time,plumed_in,velocity=velocity,temperature=temperature)
self.run(in_file,cuda,velocity=velocity)
self.run_cpptraj()
'''
traj_file = self.path_dir+'/prod'+str(index)+'_nm_nw.xtc'
top_file = 'mol_nw.prmtop'
traj_data = ana.calc_com(traj_file,top_file,bb=bb)
_,y_temp = ana.calc_fps(traj_data,time)
_,nr = ana.pick_peak(self.xf,self.y0,y_temp,ratio_threshold=ratio_threshold,top=top,window=window,freq=frequency)
'''
if rm_file:
os.system('rm '+self.path_dir+'/*mdcrd')
self.index+=1
return None
def pump(self,res_ids,mode=0,frequency=1,force=100,time=500,velocity=False,cuda='0',threshold=3,window=1,rm_file=True,bb=False,temperature=300):
'''
Run pumped md and return the pumped residues if index>0
'''
pdb_file = self.pdb
index = self.index
if index==0:
if os.path.exists('control_dist.pkl'):
f = open('control_dist.pkl','rb')
mean,std = pickle.load(f)
self.mean = mean
self.std = std
f.close()
self.index += 1
else:
print('Please run control simulation')
return None
'''
in_file = self.write_prod_input_file(time,None,velocity=velocity,temperature=temperature)
self.run(in_file,cuda,velocity=velocity)
self.run_cpptraj()
self.strip_topology_wat()
traj_file = self.path_dir+'/prod'+str(index)+'_nm_nw.xtc'
top_file = 'mol_nw.prmtop'
traj_data = ana.calc_com(traj_file,top_file,bb=bb)
self.xf,self.y0 = ana.calc_fps(traj_data,time)
f = open('control.pkl','wb')
pickle.dump([self.xf,self.y0],f)
f.close()
self.index +=1
'''
index = self.index
atom_ids = utils.get_atom_ids(pdb_file,res_ids)
vec = self.calc_nm_vec(res_ids,mode)
plumed_in = self.write_plumed_file(atom_ids,vec,frequency,force)
in_file = self.write_prod_input_file(time,plumed_in,velocity=velocity,temperature=temperature)
self.run(in_file,cuda,velocity=velocity)
self.run_cpptraj()
traj_file = self.path_dir+'/prod'+str(index)+'_nm_nw.xtc'
top_file = 'mol_nw.prmtop'
traj_data,rmsf_data = ana.calc_com(traj_file,top_file,bb=bb)
xf,y_temp = ana.calc_fps(traj_data,rmsf_data,time)
fps_temp = ana.calc_fps_at_freq(xf,y_temp,window=1,freq=frequency)
nr = ana.pick_peak_new(self.mean,self.std,fps_temp,threshold=threshold)
self.index +=1
if rm_file:
os.system('rm '+self.path_dir+'/*mdcrd')
return nr
def pump_at_res(self,res_ids,cuda='0',rm_file=True):
'''
Run pumped MD given res_id
'''
pdb_file = self.pdb
if isinstance(res_ids,int):
res_index = str(res_ids)
if isinstance(res_ids,list):
res_index = str()
for temp_id in res_ids:
res_index = res_index+'_'+str(temp_id)
atom_ids = utils.get_atom_ids(pdb_file,res_ids)
vec = self.calc_pump_vec(atom_ids)
plumed_in = self.write_plumed_file(atom_ids,vec,res_index=res_index)
prod_in = self.write_prod_input_file(plumed_in)
self.run(prod_in,cuda=cuda)
self.run_cpptraj()
self.dump_traj()
if rm_file:
os.system('rm '+self.path_dir+'/*mdcrd')
self.index+=1
return None
def write_cpptraj_vac_input_file(pdb_file, crd_file, vel_file, top_file, path):
'''
write cpptraj input file to calculate VAC for each residue
Input:
crd_file: crd file name
vel_file; vel file name
top_file: topology file name
path: path directory
'''
res_num = utils.get_res_num(pdb_file)
file_name = 'ctj_vac.in'
f = open(file_name, 'w')
f.write('parm ' + top_file + '\n')
f.write('trajin ' + crd_file + ' mdvel ' + vel_file + '\n')
for i in range(res_num):
atom_ids = utils.get_atom_ids(pdb_file, i + 1, False)
atom_ids_str_list = [str(id + 1) for id in atom_ids]
atom_mask = ','.join(atom_ids_str_list)
out_file = path + '/res_' + str(i + 1) + '_vac.dat'
f.write('velocityautocorr @' + atom_mask + ' out ' + out_file +
' tstep 0.01 norm\n')
f.close()
return None
required=True,
help=
'The ids of starting residues, saperate by \',\' no space, for example 1,2,3'
)
parser.add_argument('--end_res',
action='store',
type=str,
required=True,
help='The ids of end residues, saperate by \',\' no space')
parser.add_argument('--force',
action='store',
type=float,
required=True,
help='The amplitude of oscilation force, unit pN')
parser.add_argument(
'--frequency',
action='store',
type=float,
required=True,
help='Frequency of oscilation force, unit 1ps-1 or 10^12 Hz')
args = parser.parse_args()
start_res = args.start_res.split(',')
end_res = args.end_res.split(',')
start_res = [int(id) for id in start_res]
end_res = [int(id) for id in end_res]
index = 0
start_ids = utils.get_atom_ids(start_res)
sys.write_plumed_files(start_ids, args.frequency, args.force, index)