[gmx-users] Pairwise distances from COM of residues

Mark Abraham mark.j.abraham at gmail.com
Sat Mar 9 15:38:53 CET 2019


The gmx pairdist tool has a lot of capabilities that look like you can
already do exactly what you want, either with multiple selections or well
chosen grouping within selections. Do check the docs.


On Sat., 9 Mar. 2019, 15:00 Pandya, Akash, <akash.pandya.15 at ucl.ac.uk>

> Hi all,
> My protein is 168 amino acid residues long. I want to calculate the
> pairwise distance between the COM of each individual residue and my ligand
> molecules during my trajectory. As I have 168 amino acids, this will take
> ages if I run the gmx pairdist code each time. I was wondering whether
> there is a way to run this calculation via a script in gromacs?
> Akash
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