[gmx-users] gmx pairdist help

Pandya, Akash akash.pandya.15 at ucl.ac.uk
Tue Sep 10 19:03:03 CEST 2019

Hi all,

I'm trying calculate the pairwise distance between each of my protein residues and my ligand molecules. I type the following command:

gmx pairdist -f Traj.xtc -s Traj.tpr -n mindist.ndx -selrpos whole_res_com -refgrouping res -o dist.xvg -type min

When I don't type the "-selrpos whole_res_com" I get the same values so by default is it working out from the COM of each individual residue?


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