After performing md simulation I want to see the atomic contacts between residues. For that I have performed gmx mdmat and followed by gmx xpm2ps by using following commands
gmx mdmat -f analysis.xtc -s analysis_npt.pdb -mean mdmat.xpm -b 80000 -t 2.5
gmx xpm2ps -f mdmat.xpm -o mdmat.eps -rainbow blue -bx 10 -by 10
But I am getting some unexpected output. Actually residue numbers are missing there. I am attaching the output mdmat.eps file hope you can understand the problems of the output file. Please help me to solve such a problem.
see manual
https://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-mindist.html
Hadi Jabbar Alagealy I have followed the manual and as far I can remember have given the exact command that you can see in my question. For your consideration I am giving the command once again. Unfortunately can't find the exact reason why I am getting the faulty output. Hope you can understand that giving the link of gromacs manual is just useless here.
Can you share also the PDB file and the output of the first gmx command?
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