[gmx-users] probability density map

Erik Marklund erik.marklund at chem.ox.ac.uk
Sun Mar 23 01:04:03 CET 2014


All you need is in the hbm and hbn output.

Best regards,

Erik Marklund, PhD
Postdoctoral Research Associate

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road

On 22 Mar 2014, at 07:08, pratibha <kapoorpratibha7 at gmail.com> wrote:

> 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)?
> Thanks 
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