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