[gmx-users] Select one molecule closest to another molecule for all snapshots
jalemkul at vt.edu
Fri Feb 15 14:41:52 CET 2019
On 2/15/19 4:10 AM, Apramita Chand wrote:
> Dear Gromacs Users,
> I have two kinds of molecules in my system. I want to know the coordinates
> of the molecule A that is found closest to molecule B at every snapshot of
> the MD trajectory. I am using gromacs 5.1.
> I dont have a cutoff, I just want to generate coordinates of the single
> one molecule that is closest at any given snapshot.(for all frames0
> How do I do so? Is there any gmx tool?
> I tried '-select' statements but am not able to hit upon the right
You can use gmx trjorder to reorder the molecules in the trajectory
based on their proximity to some selected group. Then just write out the
first instance of that molecule from the trajectory using an index group
(the closest molecule will always be the first one of its type so the
index group is constant, even if it is selecting a different molecule).
Justin A. Lemkul, Ph.D.
Office: 301 Fralin Hall
Lab: 303 Engel Hall
Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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