Gibbs free energy landscape

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1

GROMACS version:
GROMACS modification: Yes/No
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I have formed gibbs free energy landscapes for my alone dna and dna ligand complex. The value for alone is 16.2 and for complex is 8.7. but the lower minimum energy colour is not prevent in complex. Please suggest. i have attached the landscapes for alone and complex
Would i select the stability of complex on the basis of color or value of energy?
also the py script is not working for 3D plots please send me the script for that for the equation
python xpm2txt.py -f fel.xpm -o fel.txt

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alone
complex

2

Hi Pallavi,
This is not a GROMACS question and I suggest you read up on free energy landscapes and statistical physics (one good book is Statistical Physics of Biomolecules by D. Zuckerman). I’m not sure where the Python script comes from, but you can surely edit it yourself to get plots in 3D. It also looks like you might need some more sampling in the second free energy plot.

3

@cathrine i am not able to understand your reply. Please reply in related to gromacs software.

4

I am pasting the script

#!/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 =
for y_index, data_value in enumerate(xpm_data):
y_value = y_axis[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()