Free energy landscape

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1

GROMACS version: 2021.5
GROMACS modification: No

I am trying to make free energy landscape plot using the gsham tool of gromacs. Everything works fine until the step in which I have to convert the .xpm file to .txt file. Whenever I convert it, a file is generated but it has very less data points for me to plot the 3d graph.

Please let me know where is the issue. I am pasting the python script I used for conversion of .xpm to .txt
#!/usr/bin/env python

import sys

“”"
Utility tool to convert xpm files generated by GROMACS to a 3-column text file.
“”"

USAGE = “USAGE: xpm2txt.py -f -o [-s]\n”
USAGE+= “Options:\n”
USAGE+= “\t-s\t(int)\tSorts the output by a given column”
USAGE+= “\n” # always keep this line

Parse arguments

read_input, read_output, sort = False, False, False
xpm_file, out_file, column_sort = None, None, None
for arg in sys.argv[1:]:
if read_input:
read_input = False
xpm_file = arg
elif read_output:
read_output = False
out_file = arg
elif sort:
sort = False
column_sort = int(arg)
if arg[0] == “-”:
if arg == “-f”:
read_input = True
continue
elif arg == “-o”:
read_output = True
continue
elif arg == “-s”:
sort = True
else:
print (USAGE)
sys.stderr.write(‘ERROR: Option not recognized: %s\n’ %arg)
sys.exit(1)

if not xpm_file:
print (USAGE)
sys.stderr.write(‘ERROR: You forgot to provide an input file.\n’)
sys.exit(1)
if not out_file:
out_file = “out.txt”

Parse XPM file

xpm_handle = open(xpm_file)
xpm_data =
x_axis, y_axis = ,
letter_to_value = {}
for line in xpm_handle:
if line.startswith(“/* x-axis”):
x_axis = map(float, line.split()[2:-2]) # We trim the last value

if line.startswith("/* y-axis"):
    y_axis = map(float, line.split()[2:-2]) # We trim the last value

if line.startswith('"') and x_axis and y_axis: # Read data
    xpm_data.insert(0, line.strip().strip(',')[1:-1])

if line.startswith('"') and len(line.split()) > 4:
    letter = line.split()[0][1:]
    value = float(line.split()[-2][1:-1])
    letter_to_value[letter] = value

xpm_handle.close()

Match x/y/data

txt_values =
y_axisFloatList = list(map(float,y_axis))
for y_index, data_value in enumerate(xpm_data):
y_value = y_axisFloatList[y_index]
for x_index, x_value in enumerate(x_axis):
txt_values.append([x_value, y_value, letter_to_value[data_value[x_index]]])

Apply sorting if requested

if column_sort:
try:
txt_values.sort(key=lambda x: x[column_sort-1])
except IndexError:
print (USAGE)
sys.stderr.write(‘ERROR: Column not found (%s)\n’ %(column_sort))
sys.exit(1)

Print to file

out_handle = open(out_file, ‘w’)
for x, y, z in txt_values:
out_handle.write(“%3.5f\t%3.5f\t%3.5f\n” %(x,y,z))
out_handle.close()

I am also pasting the .txt file with very less data points below for reference.

2.04380 2.25463 13.60000
2.04733 2.25463 13.60000
2.05085 2.25463 13.60000
2.05437 2.25463 13.60000
2.05790 2.25463 13.60000
2.06142 2.25463 12.40000
2.06495 2.25463 13.60000
2.06847 2.25463 13.60000
2.07200 2.25463 13.60000
2.07552 2.25463 13.60000
2.07904 2.25463 13.60000
2.08257 2.25463 13.60000
2.08609 2.25463 13.60000
2.08962 2.25463 13.60000
2.09314 2.25463 13.60000
2.09667 2.25463 13.60000
2.10019 2.25463 13.60000
2.10371 2.25463 13.60000
2.10724 2.25463 13.60000
2.11076 2.25463 13.60000
2.11429 2.25463 13.60000
2.11781 2.25463 13.60000
2.12134 2.25463 13.60000
2.12486 2.25463 13.60000
2.12838 2.25463 13.60000
2.13191 2.25463 13.60000
2.13543 2.25463 13.60000
2.13896 2.25463 13.60000
2.14248 2.25463 13.60000
2.14601 2.25463 13.60000
2.14953 2.25463 13.60000
2.15305 2.25463 13.60000