[gmx-users] probability density map

pratibha kapoorpratibha7 at gmail.com
Sat Mar 22 08:08:50 CET 2014

Hi all,

I would like to create 2D probability density map of backbone hydrogen bonds
between two peptide residues. Is it possible to do so using gromacs? 
I have read that g_mdmat makes distance matrices consisting of the smallest
distance between residue pairs. Is it possible to use such a tool to serve
my purpose? It asks only one group for analysis, but I want my xaxis and
yaxis to contain two different peptide residues.
Also, let me know if such a thing is possible using some other tools as well
(not sure if volmap of vmd could be of any help)?

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