Distance between COM HP-beta-cyclodextrin and Gliclazide

[alevilla]

Hi,
As far as I understand you want to calculate the distance between two or more selections. In that case gmx pairdist is better

gmx pairdist - GROMACS 2025.1 documentation

To have the com of molecule, you could define the molecule in your index file and use option like -selrpos

Here you find a brief description for the difference between gmx distance gmx pairdist

Selections for gmx distance/ gmx mindist / gmx pairdist

Hi, gmx mindist : does a selection of pollutant and surface atoms calculate the minimum distance between any pollutant atom and any surface atom at any time in my trajectory or is it somehow averaged across all residues? (i.e. in my case, if one pollutant is adsorbed but all the rest are in still solution how will this look in mindist?) gmx mindist calculates the minimum distance between the two groups at any times in the trajectory file. One group is the polluntants atoms and the other grou…

I hope it helps
Alessandra
Here you find more on Topics tagged gmx-distance