I use OpenAI to solve these issues. OpenAI can suggest a method based on python or any other program you use, like GnuPlot? Anything you use, OpenAI will provide you with the details.

Thank you for your response, Can you please share me with the script and the information regarding what input files have you used??

Use Gromacs for generating the 3D coordinates through xpm2txt.py script from the generated xpm file..

Then you can plot the same in Origin Pro software (free academic licence)

You can get the script file from (https://github.com/jobinjobzz/FEL_3D-map-generation-script.git) (Use Python2 for scripting)

Command: python2 xpm2txt.py -f gibbs.xpm -o fel.txt

Regards.....

Thank you so much jobin