def xyz2mdcrd(xyz, mdcrd):
xyzF = open(xyz, 'r')
line = xyzF.readline()
atomsNo = int(line)
mdcrdTraj = AmberMdcrd(mdcrd, atomsNo, hasbox=False, mode='w')
while line:
coordsFrame = []
xyzF.readline()
for i in range(atomsNo):
line = xyzF.readline()
for c in line.split()[-3:]:
coordsFrame.append(float(c))
mdcrdTraj.add_coordinates(coordsFrame)
line = xyzF.readline()
xyzF.close()
mdcrdTraj.close()
class Simulation():
def __init__(self, sys, MD_setting):
self.name = MD_setting.Name
self.sys = sys
self.path = './' + MD_setting.Name + '/'
self.format = MD_setting.Mdformat
self.T = MD_setting.Temp
self.maxstep = MD_setting.Mdmaxsteps
self.dt = MD_setting.Mddt
self.icap = MD_setting.Icap
self.ibox = MD_setting.Ibox
self.box = MD_setting.Box
self.center = MD_setting.Center
self.radius = MD_setting.Capradius
self.fcap = MD_setting.Capf
self.MODE = MD_setting.Mode
self.MDThermostat = MD_setting.Thermostat
self.MDV0 = MD_setting.Mdv0
self.stageindex = MD_setting.Stageindex
self.Outfile = open(
self.path + MD_setting.Name + '_%d.mdout' % self.stageindex, 'w')
self.Respfile = open(
self.path + MD_setting.Name + '_%d.resp' % self.stageindex, 'w')
self.Nprint = MD_setting.Nprint
return
def MD(self, QMQueue=None):
self.sys.Create_DisMap()
self.sys.Update_DisMap()
self.sys.update_crd()
f, e, AVG_ERR, ERROR_mols, EGCMlist, chargestr = self.sys.Cal_EFQ()
self.EPot0 = e
self.EPot = e
self.EnergyStat = OnlineEstimator(self.EPot0)
self.RealPot = 0.0
self.t = 0.0
self.KE = 0.0
self.atoms = self.sys.atoms
self.m = np.array(list(map(lambda x: ATOMICMASSES[x - 1], self.atoms)))
self.x = self.sys.coords - self.sys.coords[self.center]
self.v = np.zeros(self.x.shape)
self.a = np.zeros(self.x.shape)
self.f = f
self.md_log = None
if self.format == "Amber":
self.trajectory = AmberMdcrd(self.path + self.name +
'_%d.mdcrd' % self.stageindex,
natom=self.sys.natom,
hasbox=False,
mode='w')
self.restart = Rst7(natom=len(self.atoms))
self.trajectory.add_coordinates(self.x)
if self.MDV0 == "Random":
np.random.seed()
self.v = np.random.randn(*self.x.shape)
Tstat = Thermostat(self.m, self.v, self.T, self.dt)
elif self.MDV0 == "Thermal":
self.v = np.random.normal(size=self.x.shape) * np.sqrt(
1.38064852e-23 * self.T / self.m)[:, None]
self.Tstat = None
if (self.MDThermostat == "Rescaling"):
self.Tstat = Thermo(self.m, self.v, self.T, self.dt)
elif (self.MDThermostat == "Andersen"):
self.Tstat = Andersen(self.m, self.v, self.T, self.dt)
self.a = pow(10.0, -10.0) * np.einsum("ax,a->ax", self.f, 1.0 / self.m)
if self.format == "Amber":
self.restart.coordinates = self.x
self.restart.vels = self.v
step = 0
self.md_log = np.zeros((self.maxstep + 1, 7))
res_order = np.array(range(1, self.sys.nres))
ERROR = 0
ERROR_record = []
method_record = 0
Temp_record = []
MD_Flag = True
while step < self.maxstep and MD_Flag:
self.t += self.dt
t1 = time.time()
x_new = self.x + self.v * self.dt + 0.5 * self.a * self.dt**2
#if self.icap==True:
# x_new=x_new-x_new[self.center]
self.sys.coords = x_new
f = x_new
EPot = 0
ERROR_mols = []
self.sys.Update_DisMap()
self.sys.update_crd()
f, EPot, ERROR, ERROR_mols, EGCMlist, chargestr = self.sys.Cal_EFQ(
)
ERROR_record.append(ERROR)
if self.sys.stepmethod == 'Gaussian' and self.sys.Theroylevel == 'NN':
method_record += 1
if self.MODE == 'Train':
if QMQueue != None:
QMQueue.put(ERROR_mols)
self.EPot = EPot
distozero = np.sqrt(np.sum(self.sys.coords**2, axis=1))
if self.icap == True:
#Vec=(self.sys.Distance_Matrix[self.center]-self.radius)/self.radius
Vec = (distozero - self.radius) / self.radius
for i in range(len(x_new)):
if Vec[i] > 0:
tmpvec = (x_new[i])
tmpvec = tmpvec / np.sqrt(np.sum(tmpvec**2))
f[i] = f[i] - tmpvec * self.fcap * Vec[
i] * JOULEPERHARTREE / 627.51
f[self.
center] = f[self.center] - x_new[self.center] * 10 * Vec[
self.center] * JOULEPERHARTREE / 627.51
a_new = pow(10.0, -10.0) * np.einsum("ax,a->ax", f, 1.0 / self.m)
v_new = self.v + 0.5 * (self.a + a_new) * self.dt
if self.MDThermostat != None and step % 1 == 0:
v_new = self.Tstat.step(self.m, v_new, self.dt)
self.a = a_new
self.v = v_new
self.x = x_new
self.f = f
self.md_log[step, 0] = self.t
self.md_log[step, 4] = self.KE
self.md_log[step, 5] = self.EPot
self.md_log[
step, 6] = self.KE + (self.EPot - self.EPot0) * JOULEPERHARTREE
avE, Evar = self.EnergyStat(self.EPot)
self.KE = KineticEnergy(self.v, self.m)
Teff = (2. / 3.) * self.KE / IDEALGASR
Temp_record.append(Teff)
if (step % 50 == 0):
if self.format == "Amber":
self.trajectory.add_coordinates(self.x)
step += 1
AVG_ERR = np.mean(np.array(ERROR_record[-1000:-1]))
AVG_TEMP = np.mean(np.array(Temp_record[-1000:-1]))
#if AVG_ERR>GPARAMS.Train_setting.rmse**2*GPARAMS.Train_setting.Modelnumperpoint*4:
# MD_Flag=False
#if method_record>2:
# MD_Flag=False
if AVG_TEMP > 350:
MD_Flag = False
if (step % self.Nprint == 0):
if self.format == "Amber":
if MD_Flag:
self.restart.coordinates = self.x
self.restart.vels = self.v
self.restart.write(self.path + self.name +
'_%d.rst7' % self.stageindex)
self.steprecord = step
else:
file = open(
'%straj%d.trajin' % (self.path, self.stageindex),
'w')
file.write('trajin %s %d %d 1\n' %
(self.name + '_%d.mdcrd' % self.stageindex,
0, math.ceil(self.steprecord, 10)))
file.write('trajout %s\n' %
(self.name + '_%d.mdcrd' % self.stageindex))
os.system(
"cd %s && cpptraj -p %s < traj%d.trajin > traj%d.out && cd .."
% (self.path, self.name + '.prmtop',
self.stageindex, self.stageindex))
if MD_Flag == True:
self.Outfile.write("%s Step: %i time: %.1f(fs) KE(kJ): %.5f PotE(Eh): %.5f ETot(kJ/mol): %.5f Teff(K): %.5f MAX ERROR: %.3f Method: %s AVG_ERR: %f AVG_TEMP: %f \n"\
%(self.name, step, self.t, self.KE*len(self.m)/1000.0, self.EPot, self.KE*len(self.m)/1000.0+(self.EPot)*KJPERHARTREE, Teff,ERROR,self.sys.stepmethod,AVG_ERR,AVG_TEMP))
self.Outfile.flush()
self.Respfile.write(chargestr)
self.Respfile.write(chargestr)
else:
self.Outfile.write("AVG ERR: %.3f , MD will stop~~!!" %
AVG_ERR)
self.Outfile.flush()
self.Outfile.close()
self.Respfile.close()
return