[gmx-users] frequency of contact between all residue pairs

Erik Marklund erik.marklund at chem.ox.ac.uk
Wed Oct 21 17:09:38 CEST 2015

Hi Dina,

g_hbond -contact -hbn -hbm, then post-process the resulting contact matrix to represent residue-residue interactions.

Kind regards,

Erik Marklund, PhD
Postdoctoral Research Fellow
Fulford JRF, Somerville College

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

> On 21 Oct 2015, at 15:56, Dina Mirijanian <dmirij at brandeis.edu> wrote:
> Hello,
> I need to calculate the contact frequence between all pairs of residues in
> my protein within a certain cutoff. I was trying to figure out a way to do
> this with g_mindist.  But I have not been able to get it do what I want.
> Can someone tell me what is the best way to calculate the contact frequence
> between all residues from a trajectory?
> Thank you so much.
> -Dina
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