[gmx-users] Distance matrix between chains

Clarke, Benjamin (NIH/NIDDK) [F] benjamin.clarke at nih.gov
Tue Nov 3 17:30:12 CET 2015

Dear all,

I am analyzing a MD trajectory of a protein heterodimer and would like to identify dimer interface residues.  I have used

gmx mdmat -f md_noPBC.xtc -s md.tpr

Select Group 9 (SideChain-H)

gmx xpm2ps -f dm.xpm -o dm.eps

to create a distance matrix of all residue-residue interactions.  This is OK, but I would prefer to report just inter-Chain interactions.  Is this possible to make this with “mdmat”?  Can I plot Chain A on the y-axis and Chain B on the x-axis?


Ben Clarke

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