[gmx-users] Output frames within a defined distance range

Nash, Anthony a.nash at ucl.ac.uk
Thu Aug 6 16:15:44 CEST 2015

Hi Justin,

Cheers, that was perfect.

In case anyone comes across this in months from now, I simply performed a
gmx_d distance command which generates a .xvg of [timestamp] [distance].
This is then used as the input -drop for gmx_d trjconv. Combining with
-dropunder [mindistance] and -dropover [maxdistance], you end up with a
.trr/.xtc/.gro file with only the frames that meets your distance


Dr Anthony Nash
Department of Chemistry
University College London

On 06/08/2015 13:03, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>On 8/6/15 3:56 AM, Nash, Anthony wrote:
>> Hi all,
>> I¹m hoping to avoid putting together a simple script. Is there an option
>> in Gromacs 5+ to only output frames from a trajectory if a certain
>> criteria is meet? In this case, I only want the frames from a trajectory
>> if the carbon-alpha of a particular GLY residue is within 0.8 - 1 nm of
>> zinc ion.
>I think this is what gmx trjconv -drop -dropover/-dropunder does.  I have
>tried it, though.
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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