[gmx-users] trjconv for cutting the trajectory in small subtrajectories

Justin Lemkul jalemkul at vt.edu
Sat Apr 25 15:09:38 CEST 2015

On 4/25/15 7:52 AM, Mahboobeh Eslami wrote:
>   hi GMx user I simulated protein-ligand comolex with gromacs. total simulation time is 20ns. when I use trjconv for cutting the  trajectory  in  small   subtrajectories from 10000ps to 17000ps by following command:
> trjconv -f md.xtc -s md.tpr -n index.ndx -e 10000 -b 17000
> I see following text in terminal window;
> Reading frame       0 time 10000.000
> Precision of md-nopbc.xtc is 0.001 (nm)
> Using output precision of 0.001 (nm)
>   ->  frame   3500 time 17000.000        ->  frame   3000 time 16000.000

The output frame number doesn't necessarily reflect what's actually written; 
it's just a simple progress indicator.  Use gmxcheck to verify the contents of 
the new trajectory.



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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