[gmx-users] g_mindist works along trajectory? (gromacs 4.6)

ms devicerandom at gmail.com
Wed Aug 27 20:10:22 CEST 2014

Dear Gromacs users,

I am using Gromacs 4.6. I would like to plot the contacts (minimum 
atom-atom distances) between some residue side chains and a ligand along 
a trajectory. I thought I would find the solution in g_dist or 
g_mindist, however, if I understand correctly:

- g_dist calculates the distances between the *center of mass* of a 
group (say, the residue) and another (say, the ligand). This is not 
really what I want, since I want the *minimum* distance between the two 
groups, to declare it a contact or not.
- g_mindist calculates the minimum distance between the two groups ; 
however it seems to me it does give the minimum distance along *all* the 
trajectory, not for each individual frame. Am I wrong?

In short, what's the best strategy to accomplish what I am trying to do?

Many thanks for your help,

More information about the gromacs.org_gmx-users mailing list