def main():
water_charges = {"t3p" : [-0.834, 0.417, 0.417], "pm6" : [-2.000, 1.000, 1.000]}
prefix = sys.argv[1]
curr_dir = os.getcwd()
n_conf = 5
n_runs = 1
charge_sets = ["t3p", "pm6"]
chg = sys.argv[1]
if chg not in charge_sets:
sys.exit("Charge set %s not allowed!" % chg)
charges = water_charges[chg]
# input files
data_dir = os.path.abspath("../data/gramicidin/simulations/input_struct_%s" % chg)
mu = []
amide_mu = []
for n in range(n_runs):
mu_z = []
prefix = "run_%02d" % n
print("Processing %s:" % prefix)
msdat = os.path.join(data_dir, prefix, "ms.dat")
head3lst = os.path.join(data_dir, prefix, "head3.lst")
fort38 = os.path.join(data_dir, prefix, "fort.38")
energies_opp = os.path.join(data_dir, prefix, "energies.opp")
step2out = os.path.join(data_dir, prefix, "step2_out.pdb")
msa = Simulation(msdat, head3lst, fort38)
msa.parse_trajectory(sample_frequency=10)
msa.parse_struct(step2out, n_conf)
msa.calculate_water_dipoles(charges)
def calc_muz(n, n_conf, chg, charges, data_dir, save=False, save_freq=1000):
mu_z = []
prefix = "run_%02d" % n
print("Processing %s:" % prefix)
msdat = os.path.join(data_dir, prefix, "ms.dat")
head3lst = os.path.join(data_dir, prefix, "head3.lst")
fort38 = os.path.join(data_dir, prefix, "fort.38")
energies_opp = os.path.join(data_dir, prefix, "energies.opp")
step2out = os.path.join(data_dir, prefix, "step2_out.pdb")
msa = Simulation(msdat, head3lst, fort38)
msa.parse_trajectory(sample_frequency=100)
msa.parse_struct(step2out, n_conf)
msa.calculate_water_dipoles(charges)
pdb_save_dir = os.path.abspath("pdbs/apolar_gram_%s/%s" % (chg, prefix))
if not os.path.exists(pdb_save_dir):
os.makedirs(pdb_save_dir)
for i in range(msa.trajectory.shape[0]):
microstate_conf_ids = msa.trajectory[i, :]
wat_ids = []
dps = []
for c in microstate_conf_ids:
dp = msa.conformer_data[msa.conf_id_name_map[c + 1]][-1]
if dp is not None:
dps.append(dp)
wat_ids.extend(msa.conformer_data[msa.conf_id_name_map[c +
1]][2])
mu_z.append(dps)
t_dp = sum(dps)
if save:
if not i % save_freq:
print("Saving config %d with dipole %g." % (i, sum(dps)))
print("Energy = %g" % msa.energies[i])
snapshot_st = msa.structure.atom_slice(wat_ids)
snapshot_st.save_pdb("%s/%05d_config.pdb" % (pdb_save_dir, i))
print("Microstate %d: Energy = %g, Dipole = %g" %
(i, msa.energies[i], t_dp))
mu_z = np.array([np.cumsum(m) for m in mu_z])
return mu_z
def main():
water_charges = {"t3p" : [-0.834, 0.417, 0.417], "pm6" : [-2.000, 1.000, 1.000]}
prefix = sys.argv[1]
curr_dir = os.getcwd()
n_conf = 1
charge_sets = ["t3p", "pm6"]
chg = sys.argv[1]
if chg not in charge_sets:
sys.exit("Charge set %s not allowed!" % chg)
charges = water_charges[chg]
# input files
data_dir = os.path.abspath("../data/gramicidin/simulations/mc_type")
msdat = os.path.join(data_dir, prefix + "_ms.dat")
head3lst = os.path.join(data_dir, prefix + "_head3.lst")
fort38 = os.path.join(data_dir, prefix + "_fort.38")
energies_opp = os.path.join(data_dir, prefix + "_energies.opp")
step2out = os.path.join(data_dir, "step2_out.pdb")
msa = Simulation(msdat, head3lst, fort38)
msa.parse_trajectory(sample_frequency=1)
msa.parse_struct(step2out, n_conf)
msa.calculate_water_dipoles(charges)
mu_z = []
for i in range(msa.trajectory.shape[0]):
microstate_conf_ids = msa.trajectory[i, :]
wat_ids = []
dps = []
for c in microstate_conf_ids:
dp = msa.conformer_data[msa.conf_id_name_map[c + 1]][-1]
if dp is not None:
dps.append(dp)
wat_ids.extend(msa.conformer_data[msa.conf_id_name_map[c + 1]][2])
mu_z.append(dps)
t_dp = sum(dps)
#if t_dp > -0.2 and t_dp < 0.2:
#print("Found config %d with desired dipole %g, saving.." % (i, sum(dps)))
#print("Energy = %g" % msa.energies[i])
#snapshot_st = msa.structure.atom_slice(wat_ids)
#snapshot_st.save_pdb("test_pdbs/%05d_config.pdb" % i)
#print("Microstate %d: Energy = %g, Dipole = %g" % (i, msa.energies[i], t_dp))
mu_z = np.array([sum(m) for m in mu_z])
figure = pylab.figure(figsize=(7.5, 3.5), dpi=300)
y, bin_edges = np.histogram(mu_z, bins=50)
kernel = stats.gaussian_kde(mu_z)
bin_centers = 0.5 * (bin_edges[1:] + bin_edges[:-1])
plt.hist(mu_z, bins=50, normed=1, histtype='stepfilled')
p_y = kernel.evaluate(bin_centers)
plt.plot(bin_centers, p_y, 'k-')
plt.xlim(-4.0, 4.0)
#plt.ylim(0.0, np.max(p_x) + 0.1)
plt.ylim(0.0, 1.2)
plt.xlabel(r'$\mu_{z,total}$', size=14)
plt.ylabel(r'$P(\mu_{z,total})$', size=14)
plt.tight_layout()
plt.savefig("sim_07_%s_histogram_total_dipole.png" % str(chg))
os.chdir(curr_dir)
def main():
water_charges = {
"t3p": [-0.834, 0.417, 0.417],
"pm6": [-2.000, 1.000, 1.000]
}
prefix = sys.argv[1]
curr_dir = os.getcwd()
n_conf = 5
n_runs = 10
charge_sets = ["t3p", "pm6"]
chg = sys.argv[1]
if chg not in charge_sets:
sys.exit("Charge set %s not allowed!" % chg)
charges = water_charges[chg]
# input files
data_dir = os.path.abspath(
"../data/gramicidin/simulations/apolar_gram_%s" % chg)
mu = []
amide_mu = []
for n in range(n_runs):
mu_z = []
prefix = "run_%02d" % n
print("Processing %s:" % prefix)
msdat = os.path.join(data_dir, prefix, "ms.dat")
head3lst = os.path.join(data_dir, prefix, "head3.lst")
fort38 = os.path.join(data_dir, prefix, "fort.38")
energies_opp = os.path.join(data_dir, prefix, "energies.opp")
step2out = os.path.join(data_dir, prefix, "step2_out.pdb")
msa = Simulation(msdat, head3lst, fort38)
msa.parse_trajectory(sample_frequency=10)
msa.parse_struct(step2out, n_conf)
msa.calculate_water_dipoles(charges)
test = calc_amide_dipole(step2out)
pdb_save_dir = os.path.abspath("pdbs/apolar_gram_%s/%s" %
(chg, prefix))
if not os.path.exists(pdb_save_dir):
os.makedirs(pdb_save_dir)
for i in range(msa.trajectory.shape[0]):
microstate_conf_ids = msa.trajectory[i, :]
wat_ids = []
dps = []
for c in microstate_conf_ids:
dp = msa.conformer_data[msa.conf_id_name_map[c + 1]][-1]
if dp is not None:
dps.append(dp)
wat_ids.extend(
msa.conformer_data[msa.conf_id_name_map[c + 1]][2])
mu_z.append(dps)
t_dp = sum(dps)
#if not i % 1000:
#print("Saving config %d with dipole %g." % (i, sum(dps)))
#print("Energy = %g" % msa.energies[i])
#snapshot_st = msa.structure.atom_slice(wat_ids)
#snapshot_st.save_pdb("%s/%05d_config.pdb" % (pdb_save_dir, i))
#print("Microstate %d: Energy = %g, Dipole = %g" % (i, msa.energies[i], t_dp))
mu_z = np.array([sum(m) for m in mu_z])
mu.append(np.mean(mu_z))
amide_mu.append(test)
figure = pylab.figure(figsize=(7.5, 3.5), dpi=300)
y, bin_edges = np.histogram(mu_z, bins=50)
kernel = stats.gaussian_kde(mu_z)
bin_centers = 0.5 * (bin_edges[1:] + bin_edges[:-1])
plt.hist(mu_z, bins=50, normed=1, histtype='stepfilled')
p_y = kernel.evaluate(bin_centers)
plt.plot(bin_centers, p_y, 'k-')
plt.xlim(-6.0, 6.0)
plt.ylim(0.0, np.max(p_y) + 0.2)
#plt.ylim(0.0, 1.2)
style = dict(size=10, color='gray')
plt.text(-5.8, 0.1, "%.2f" % test, **style)
plt.xlabel(r'$\mu_{z,total}$', size=14)
plt.ylabel(r'$P(\mu_{z,total})$', size=14)
plt.tight_layout()
plt.savefig("%s_sim_04_%s" % (chg + "_apolar_gram_", prefix))
os.chdir(curr_dir)
figure = pylab.figure(figsize=(4.5, 4.5), dpi=300)
plt.scatter(mu, amide_mu)
plt.xlabel(r'$\mu_{z,water}$', size=14)
plt.ylabel(r'$\mu_{z,amide}$', size=14)
plt.tight_layout()
mu = []
ab_indices = []
n_wat = []
dipole_x = []
dipole_y = []
dipole_z = []
data_dir = '/home/yzhang/Dropbox/ProtonHopping/data/gramicidin/simulations/input_struct_dp_groups_positive_t3p'
prefix = "run_restart200_000001_1_update"
print("Processing %s:" % prefix)
msdat = os.path.join(data_dir, prefix, "ms.dat")
head3lst = os.path.join(data_dir, prefix, "head3.lst")
fort38 = os.path.join(data_dir, prefix, "fort.38")
step2out = os.path.join(data_dir, prefix, "step2_out.pdb")
msa = Simulation(msdat, head3lst, fort38)
msa.parse_trajectory(sample_frequency=10)
msa.parse_struct(step2out)
conf_dipoles = msa.calculate_dipoles()
print(conf_dipoles['HOH01W0233_006'])
numbers = zeros(msa.trajectory.shape[0], dtype="int64")
for i in range(msa.trajectory.shape[0]):
microstate_conf_ids = msa.trajectory[i, :]
numbers[i] = msa.state_counts[i]
dps = []
curr_wat_ids = []
for index, c in enumerate(microstate_conf_ids):
conf_name = msa.conf_id_name_map[c + 1]
if "DM" not in conf_name:
dpX = conf_dipoles[conf_name][0]
dpY = conf_dipoles[conf_name][1]