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

Smith, Micholas D. smithmd at ornl.gov
Thu Aug 6 14:01:23 CEST 2015


As far as I am aware, no. You could use gmx select to find the frames where the crietria is met  though and use that to extract the frames from a script, which is faster than loading into a viewer (vmd for instance) and extracting frames.


Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Nash, Anthony <a.nash at ucl.ac.uk>
Sent: Thursday, August 06, 2015 3:56 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Output frames within a defined distance range

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 a
zinc ion.

Many thanks

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