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amber-mden-analyzer.py
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#!/usr/bin/python
#***************************************************************************
# amber_mden_analyzer.py
# - Python script for the transformation of mden to a XY file for
# graphic display
# -------------------
# begin : Wed Mar 21 2007
# copyright : (C) 2004 by Nelson Fonseca
# email : nfonseca@dq.ua.pt
# ***************************************************************************/
#/***************************************************************************
# * *
# * This program is free software; you can redistribute it and/or modify *
# * it under the terms of the GNU General Public License as published by *
# * the Free Software Foundation; either version 2 of the License, or *
# * (at your option) any later version. *
# * *
# ***************************************************************************/
#V0.1 21/03/2007
############################
# import modules #
############################
import string # import string module
import re # import regular expression module
from array import * # import everything from array module
###########################
# input #
###########################
mden=raw_input("Enter Input File Name: ")
timestep=float(raw_input("Enter the Time Step: ")) # time step used in the MD
ntwe=int(raw_input("Enter the Value of ntwe: ")) # output frequency of the mden file
file_input=open(mden)
lines=file_input.read() # loads the entire file in one list of strings
lines_split=lines.split() # splits the list in multiple strings with space delimiter by default
del lines_split[0:51] # remove headers lines
####################################
# FILES FROM OUTPUT RESULTS #
####################################
Nsteps_file=open("Nsteps.txt","w")
Nsteps_file.write("#""\t""Nsteps""\t\t""time (ps)""\n")
Etot_file=open("Etot.txt","w")
Etot_file.write("#""\t""time (ps)""\t""Etot (kcal/mol""\t\t""<Etot>""\n")
EKinetic_file=open("EKinetic.txt","w")
EKinetic_file.write("#""\t""time (ps)""\t""EKinetic (kcal/mmol)""\t\t""<EKinetic>""\n")
Temp_file=open("Temp.txt","w")
Temp_file.write("#""\t""time (ps)""\t""Temp (K)""\t\t\t""<Temp>""\n")
T_solute_file=open("T_solute.txt","w")
T_solute_file.write("#""\t""time (ps)""\t""T_solute (K)""\t\t""<T_solute>""\n")
T_solv_file=open("T_solv.txt","w")
T_solv_file.write("#""\t""time (ps)""\t""T_solv (K)""\t\t\t""<T_solv>""\n")
Pres_scal_solu_file=open("Pres_scal_solu.txt","w")
Pres_scal_solu_file.write("#""\t""time (ps)""\t""Pres_scal_solu""\t\t""<Pres_scal_solu>""\n")
Pres_scal_solv_file=open("Pres_scal_solv.txt","w")
Pres_scal_solv_file.write("#""\t""time (ps)""\t""Pres_scal_solv""\t\t""<Pres_scal_solv>""\n")
BoxX_file=open("BoxX.txt","w")
BoxX_file.write("#""\t""time (ps)""\t""BoxX""\t\t\t""<BoxX>""\n")
BoxY_file=open("BoxY.txt","w")
BoxY_file.write("#""\t""time (ps)""\t""BoxY""\t\t\t""<BoxY>""\n")
BoxZ_file=open("BoxZ.txt","w")
BoxZ_file.write("#""\t""time (ps)""\t""BoxZ""\t\t\t""<BoxZ>""\n")
volume_file=open("volume.txt","w")
volume_file.write("#""\t""time (ps)""\t""volume (A^3)""\t\t""<volume>""\n")
pres_X_file=open("pres_X.txt","w")
pres_X_file.write("#""\t""time (ps)""\t""pres_X""\t\t\t""<pres_X>""\n")
pres_Y_file=open("pres_Y.txt","w")
pres_Y_file.write("#""\t""time (ps)""\t""pres_Y""\t\t\t""<pres_Y>""\n")
pres_Z_file=open("pres_Z.txt","w")
pres_Z_file.write("#""\t""time (ps)""\t""pres_Z""\t\t\t""<pres_Z>""\n")
Pressure_file=open("Pressure.txt","w")
Pressure_file.write("#""\t""time (ps)""\t""Pressure""\t\t""<Pressure>""\n")
EKCoM_x_file=open("EKCoM_x.txt","w")
EKCoM_x_file.write("#""\t""time (ps)""\t""EKCoM_x""\t\t\t""<EKCoM_x>""\n")
EKCoM_y_file=open("EKCoM_y.txt","w")
EKCoM_y_file.write("#""\t""time (ps)""\t""EKCoM_y""\t\t\t""<EKCoM_y>""\n")
EKCoM_z_file=open("EKCoM_z.txt","w")
EKCoM_z_file.write("#""\t""time (ps)""\t""EKCoM_z""\t\t\t""<EKCoM_z>""\n")
EKComTot_file=open("EKComTot.txt","w")
EKComTot_file.write("#""\t""time (ps)""\t""EKComTot""\t\t""<EKComTot>""\n")
VIRIAL_x_file=open("VIRIAL_x.txt","w")
VIRIAL_x_file.write("#""\t""time (ps)""\t""VIRIAL_x""\t\t""<VIRIAL_x>""\n")
VIRIAL_y_file=open("VIRIAL_y.txt","w")
VIRIAL_y_file.write("#""\t""time (ps)""\t""VIRIAL_y""\t\t""<VIRIAL_y>""\n")
VIRIAL_z_file=open("VIRIAL_z.txt","w")
VIRIAL_z_file.write("#""\t""time (ps)""\t""VIRIAL_z""\t\t""<VIRIAL_z>""\n")
VIRIAL_tot_file=open("VIRIAL_tot.txt","w")
VIRIAL_tot_file.write("#""\t""time (ps)""\t""VIRIAL_tot""\t\t""<VIRIAL_tot>""\n")
E_pot_file=open("E_pot.txt","w")
E_pot_file.write("#""\t""time (ps)""\t""E_pot (kcal/mol)""\t\t""<E_pot>""\n")
E_vdw_file=open("E_vdw.txt","w")
E_vdw_file.write("#""\t""time (ps)""\t""E_vdw (kcal/mol)""\t\t""<E_vdw>""\n")
E_el_file=open("E_el.txt","w")
E_el_file.write("#""\t""time (ps)""\t""E_el (kcal/mol)""\t\t\t""<E_el>""\n")
E_hbon_file=open("E_hbon.txt","w")
E_hbon_file.write("#""\t""time (ps)""\t""E_hbon (kcal/mol)""\t\t""<E_hbon>""\n")
E_bon_file=open("E_bon.txt","w")
E_bon_file.write("#""\t""time (ps)""\t""E_bon (kcal/mol)""\t\t""<E_bon>""\n")
E_angle_file=open("E_angle.txt","w")
E_angle_file.write("#""\t""time (ps)""\t""E_angle (kcal/mol)""\t\t""<E_angle>""\n")
E_dih_file=open("E_dih.txt","w")
E_dih_file.write("#""\t""time (ps)""\t""E_dih (kcal/mol)""\t\t""<E_dih>""\n")
E_14vdw_file=open("E_14vdw.txt","w")
E_14vdw_file.write("#""\t""time (ps)""\t""E_14vdw (kcal/mol)""\t\t""<E_14vdw>""\n")
E_14el_file=open("E_14el.txt","w")
E_14el_file.write("#""\t""time (ps)""\t""E_14el (kcal/mol)""\t\t""<E_14el>""\n")
E_const_file=open("E_const.txt","w")
E_const_file.write("#""\t""time (ps)""\t""E_const (kcal/mol)""\t\t""<E_const>""\n")
E_pol_file=open("E_pol.txt","w")
E_pol_file.write("#""\t""time (ps)""\t""E_pol (kcal/mol)""\t\t""<E_pol>""\n")
AV_permMoment_file=open("AV_permMoment.txt","w")
AV_permMoment_file.write("#""\t""time (ps)""\t""AV_permMoment""\t\t""<AV_permMoment>""\n")
AV_indMoment_file=open("AV_indMoment.txt","w")
AV_indMoment_file.write("#""\t""time (ps)""\t""AV_indMoment""\t\t""<AV_indMoment>""\n")
AV_totMoment_file=open("AV_totMoment.txt","w")
AV_totMoment_file.write("#""\t""time (ps)""\t""AV_totMoment""\t\t""<AV_totMoment>""\n")
Density_file=open("Density.txt","w")
Density_file.write("#""\t""time (ps)""\t""Density (g/cm^3)""\t\t""<Density>""\n")
dV_dlambda_file=open("dV_dlambda.txt","w")
dV_dlambda_file.write("#""\t""time (ps)""\t""dV/dlambda""\t\t""<dV/dlambda>""\n")
###########################
# #
# Loops over file #
###########################
j=0 # time counter
i=0 # Nstep counter
step=0 # initialize step
while i < len(lines_split) or j < len(lines_split):
Nsteps=lines_split[i]
time=lines_split[j]
timetemp=timestep*ntwe*step
i=i+51
j=j+51
Nsteps_file.write("\t" + str(step) + "\t" + str(timetemp) + "\n")
step=step+1
print "\nOutputing..."
j=2 # reinitialize time counter
k=3 # set Etot counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_Etot=array("f")
while j<len(lines_split) or k<len(lines_split) :
time=float(lines_split[j])
Etot=float(lines_split[k])
matrix_Etot.append(Etot)
sum=sum+Etot
average=sum/len(matrix_Etot)
timetemp=timestep*ntwe*step
Etot_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%Etot) + "\t\t" + str('%.3f'%average) + "\n")
j=j+51
k=k+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
l=4 # EKinetic counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_EKinetic=array("f")
while j<len(lines_split) or l<len(lines_split) :
time=float(lines_split[j])
EKinetic=float(lines_split[l])
matrix_EKinetic.append(EKinetic)
sum=sum+EKinetic
average=sum/len(matrix_EKinetic)
timetemp=timestep*ntwe*step
EKinetic_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%EKinetic) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
l=l+51
print "Outputing..."
j=2 # reinitialize time counter
m=6 # Temp counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_Temp=array("f")
while j<len(lines_split) or m<len(lines_split) :
time=float(lines_split[j])
Temp=float(lines_split[m])
matrix_Temp.append(Temp)
sum=sum+Temp
average=sum/len(matrix_Temp)
timetemp=timestep*ntwe*step
Temp_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%Temp) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
m=m+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
n=7 # T_solute counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_T_solute=array("f")
while j<len(lines_split) or n<len(lines_split) :
time=float(lines_split[j])
T_solute=float(lines_split[n])
matrix_T_solute.append(T_solute)
sum=sum+T_solute
average=sum/len(matrix_T_solute)
timetemp=timestep*ntwe*step
T_solute_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%T_solute) + "\t\t" + str('%.3f'%average) + "\n")
j=j+51
n=n+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
o=8 # T_solv counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_T_solv=array("f")
while j<len(lines_split) or o<len(lines_split) :
time=float(lines_split[j])
T_solv=float(lines_split[o])
matrix_T_solv.append(T_solv)
sum=sum+T_solv
average=sum/len(matrix_T_solv)
timetemp=timestep*ntwe*step
T_solv_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%T_solv) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
o=o+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
p=9 # Pres_scal_solu counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_Pres_scal_solu=array("f")
while j<len(lines_split) or p<len(lines_split) :
time=float(lines_split[j])
Pres_scal_solu=float(lines_split[p])
matrix_Pres_scal_solu.append(Pres_scal_solu)
sum=sum+Pres_scal_solu
average=sum/len(matrix_Pres_scal_solu)
timetemp=timestep*ntwe*step
Pres_scal_solu_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%Pres_scal_solu) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
p=p+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
q=11 # Pres_scal_solv counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_Pres_scal_solv=array("f")
while j<len(lines_split) or q<len(lines_split) :
time=float(lines_split[j])
Pres_scal_solv=float(lines_split[q])
matrix_Pres_scal_solv.append(Pres_scal_solv)
sum=sum+Pres_scal_solv
average=sum/len(matrix_Pres_scal_solv)
timetemp=timestep*ntwe*step
Pres_scal_solv_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%Pres_scal_solv) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
q=q+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
r=12 # BoxX counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_BoxX=array("f")
while j<len(lines_split) or r<len(lines_split) :
time=float(lines_split[j])
BoxX=float(lines_split[r])
matrix_BoxX.append(BoxX)
sum=sum+BoxX
average=sum/len(matrix_BoxX)
timetemp=timestep*ntwe*step
BoxX_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%BoxX) + "\t\t" + str('%.3f'%average) + "\n")
j=j+51
r=r+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
s=13 # BoxY counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_BoxY=array("f")
while j<len(lines_split) or s<len(lines_split) :
time=float(lines_split[j])
BoxY=float(lines_split[s])
matrix_BoxY.append(BoxY)
sum=sum+BoxY
average=sum/len(matrix_BoxY)
timetemp=timestep*ntwe*step
BoxY_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%BoxY) +"\t\t" + str('%.3f'%average) + "\n")
j=j+51
s=s+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
t=14 # BoxZ counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_BoxZ=array("f")
while j<len(lines_split) or t<len(lines_split) :
time=float(lines_split[j])
BoxZ=float(lines_split[t])
matrix_BoxZ.append(BoxZ)
sum=sum+BoxZ
average=sum/len(matrix_BoxZ)
timetemp=timestep*ntwe*step
BoxZ_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%BoxZ) + "\t\t" + str('%.3f'%average) + "\n")
j=j+51
t=t+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
u=16 # volume counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_volume=array("f")
while j<len(lines_split) or u<len(lines_split) :
time=float(lines_split[j])
volume=float(lines_split[u])
matrix_volume.append(volume)
sum=sum+volume
average=sum/len(matrix_volume)
timetemp=timestep*ntwe*step
volume_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%volume) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
u=u+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
v=17 # pres_X counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_pres_X=array("f")
while j<len(lines_split) or v<len(lines_split) :
time=float(lines_split[j])
pres_X=float(lines_split[v])
matrix_pres_X.append(pres_X)
sum=sum+pres_X
average=sum/len(matrix_pres_X)
timetemp=timestep*ntwe*step
pres_X_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%pres_X) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
v=v+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
w=18 # pres_Y counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_pres_Y=array("f")
while j<len(lines_split) or w<len(lines_split) :
time=float(lines_split[j])
pres_Y=float(lines_split[w])
matrix_pres_Y.append(pres_Y)
sum=sum+pres_Y
average=sum/len(matrix_pres_Y)
timetemp=timestep*ntwe*step
pres_Y_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%pres_Y) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
w=w+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
y=19 # pres_Z counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_pres_Z=array("f")
while j<len(lines_split) or y<len(lines_split) :
time=float(lines_split[j])
pres_Z=float(lines_split[y])
matrix_pres_Z.append(pres_Z)
sum=sum+pres_Z
average=sum/len(matrix_pres_Z)
timetemp=timestep*ntwe*step
pres_Z_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%pres_Z) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
y=y+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
z=21 # Pressure counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_Pressure=array("f")
while j<len(lines_split) or z<len(lines_split) :
time=float(lines_split[j])
Pressure=float(lines_split[z])
matrix_Pressure.append(Pressure)
sum=sum+Pressure
average=sum/len(matrix_Pressure)
timetemp=timestep*ntwe*step
Pressure_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%Pressure) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
z=z+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
kk=22 # EKCoM_x counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_EKCoM_x=array("f")
while j<len(lines_split) or kk<len(lines_split) :
time=float(lines_split[j])
EKCoM_x=float(lines_split[kk])
matrix_EKCoM_x.append(EKCoM_x)
sum=sum+EKCoM_x
average=sum/len(matrix_EKCoM_x)
timetemp=timestep*ntwe*step
EKCoM_x_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%EKCoM_x) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
kk=kk+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
ll=23 # EKCoM_y counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_EKCoM_y=array("f")
while j<len(lines_split) or ll<len(lines_split) :
time=float(lines_split[j])
EKCoM_y=float(lines_split[ll])
matrix_EKCoM_y.append(EKCoM_y)
sum=sum+EKCoM_y
average=sum/len(matrix_EKCoM_y)
timetemp=timestep*ntwe*step
EKCoM_y_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%EKCoM_y) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
ll=ll+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
mm=24 # EKCoM_Z counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_EKCoM_z=array("f")
while j<len(lines_split) or mm<len(lines_split) :
time=float(lines_split[j])
EKCoM_z=float(lines_split[mm])
matrix_EKCoM_z.append(EKCoM_z)
sum=sum+EKCoM_z
average=sum/len(matrix_EKCoM_z)
timetemp=timestep*ntwe*step
EKCoM_z_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%EKCoM_z) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
mm=mm+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
nn=26 # EKComTot counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_EKComTot=array("f")
while j<len(lines_split) or nn<len(lines_split) :
time=float(lines_split[j])
EKComTot=float(lines_split[nn])
matrix_EKComTot.append(EKComTot)
sum=sum+EKComTot
average=sum/len(matrix_EKComTot)
timetemp=timestep*ntwe*step
EKComTot_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%EKComTot) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
nn=nn+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
oo=27 # VIRIAL_x counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_VIRIAL_x=array("f")
while j<len(lines_split) or oo<len(lines_split) :
time=float(lines_split[j])
VIRIAL_x=float(lines_split[oo])
matrix_VIRIAL_x.append(VIRIAL_x)
sum=sum+VIRIAL_x
average=sum/len(matrix_VIRIAL_x)
timetemp=timestep*ntwe*step
VIRIAL_x_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%VIRIAL_x) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
oo=oo+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
pp=28 # VIRIAL_y counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_VIRIAL_y=array("f")
while j<len(lines_split) or pp<len(lines_split) :
time=float(lines_split[j])
VIRIAL_y=float(lines_split[pp])
matrix_VIRIAL_y.append(VIRIAL_y)
sum=sum+VIRIAL_y
average=sum/len(matrix_VIRIAL_y)
timetemp=timestep*ntwe*step
VIRIAL_y_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%VIRIAL_y) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
pp=pp+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
qq=29 # VIRIAL_z counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_VIRIAL_z=array("f")
while j<len(lines_split) or qq<len(lines_split) :
time=float(lines_split[j])
VIRIAL_z=float(lines_split[qq])
matrix_VIRIAL_z.append(VIRIAL_z)
sum=sum+VIRIAL_z
average=sum/len(matrix_VIRIAL_z)
timetemp=timestep*ntwe*step
VIRIAL_z_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%VIRIAL_z) +"\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
qq=qq+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
rr=31 # VIRIAL_tot counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_VIRIAL_tot=array("f")
while j<len(lines_split) or rr<len(lines_split) :
time=float(lines_split[j])
VIRIAL_tot=float(lines_split[rr])
matrix_VIRIAL_tot.append(VIRIAL_tot)
sum=sum+VIRIAL_tot
average=sum/len(matrix_VIRIAL_tot)
timetemp=timestep*ntwe*step
VIRIAL_tot_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%VIRIAL_tot) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
rr=rr+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
ss=32 # E_pot counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_E_pot=array("f")
while j<len(lines_split) or ss<len(lines_split) :
time=float(lines_split[j])
E_pot=float(lines_split[ss])
matrix_E_pot.append(E_pot)
sum=sum+E_pot
average=sum/len(matrix_E_pot)
timetemp=timestep*ntwe*step
E_pot_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%E_pot) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
ss=ss+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
tt=33 # E_vdw counterE_bon
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_E_vdw=array("f")
while j<len(lines_split) or tt<len(lines_split) :
time=float(lines_split[j])
E_vdw=float(lines_split[tt])
matrix_E_vdw.append(E_vdw)
sum=sum+E_vdw
average=sum/len(matrix_E_vdw)
timetemp=timestep*ntwe*step
E_vdw_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%E_vdw) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
tt=tt+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
uu=34 # E_el counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_E_el=array("f")
while j<len(lines_split) or uu<len(lines_split) :
time=float(lines_split[j])
E_el=float(lines_split[uu])
matrix_E_el.append(E_el)
sum=sum+E_el
average=sum/len(matrix_E_el)
timetemp=timestep*ntwe*step
E_el_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%E_el) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
uu=uu+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
vv=36 # E_hbon counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_E_hbon=array("f")
while j<len(lines_split) or vv<len(lines_split) :
time=float(lines_split[j])
E_hbon=float(lines_split[vv])
matrix_E_hbon.append(E_hbon)
sum=sum+E_hbon
average=sum/len(matrix_E_hbon)
timetemp=timestep*ntwe*step
E_hbon_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%E_hbon) + "\t\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
vv=vv+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
ww=37 # E_bon counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_E_bon=array("f")
while j<len(lines_split) or ww<len(lines_split) :
time=float(lines_split[j])
E_bon=float(lines_split[ww])
matrix_E_bon.append(E_bon)
sum=sum+E_bon
average=sum/len(matrix_E_bon)
timetemp=timestep*ntwe*step
E_bon_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%E_bon) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
ww=ww+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
yy=38 # E_angle counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_E_angle=array("f")
while j<len(lines_split) or yy<len(lines_split) :
time=float(lines_split[j])
E_angle=float(lines_split[yy])
matrix_E_angle.append(E_angle)
sum=sum+E_angle
average=sum/len(matrix_E_angle)
timetemp=timestep*ntwe*step
E_angle_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%E_angle) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
yy=yy+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
zz=39 # E_dih counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_E_dih=array("f")
while j<len(lines_split) or zz<len(lines_split) :
time=float(lines_split[j])
E_dih=float(lines_split[zz])
matrix_E_dih.append(E_dih)
sum=sum+E_dih
average=sum/len(matrix_E_dih)
timetemp=timestep*ntwe*step
E_dih_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%E_dih) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
zz=zz+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
kkk=41 # E_14vdw counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_E_14vdw=array("f")
while j<len(lines_split) or kkk<len(lines_split) :
time=float(lines_split[j])
E_14vdw=float(lines_split[kkk])
matrix_E_14vdw.append(E_14vdw)
sum=sum+E_14vdw
average=sum/len(matrix_E_14vdw)
timetemp=timestep*ntwe*step
E_14vdw_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%E_14vdw) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
kkk=kkk+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
lll=42 # E_14el counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_E_14el=array("f")
while j<len(lines_split) or lll<len(lines_split) :
time=float(lines_split[j])
E_14el=float(lines_split[lll])
matrix_E_14el.append(E_14el)
sum=sum+E_14el
average=sum/len(matrix_E_14el)
timetemp=timestep*ntwe*step
E_14el_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%E_14el) + "\t\t\t" + str('%.3f'%average) + "\n")
j=j+51
lll=lll+51
step=step+1
print "Outputing..."
j=2 # reinitialize time counter
mmm=43 # E_const counter
sum=0.0 # initial sum counter for averages
step=0 # initialize step
matrix_E_const=array("f")
while j<len(lines_split) or mmm<len(lines_split) :
time=float(lines_split[j])
E_const=float(lines_split[mmm])
matrix_E_const.append(E_const)
sum=sum+E_const
average=sum/len(matrix_E_const)
timetemp=timestep*ntwe*step
E_const_file.write("\t" + str(timetemp) + "\t\t" + str('%.3f'%E_const) + "\t\t\t\t" + str('%.3f'%average) + "\n")
j=j+51