[gmx-users] trjconv problem

Justin A. Lemkul jalemkul at vt.edu
Thu May 5 17:22:38 CEST 2011

Sanku M wrote:
> Hi,
>   I am having a problem with trjconv to get a single snap-shot from a 
> trajectory file. I am using gromacs 4.0.7 .
> If I try to get a snapshot corresponding to 14 ps, I was trying to use 
>  "-b 14 -e 14 " command as follows. But,
> If I issue this command as shown below
> trjconv --f  traj.xtc -o  conf_pep.gro -s topol.tpr  -b 14.0 -e 14.0 
>  it crashes with following error:
> Precision of traj.xtc is 0.001 (nm)
> Using output precision of 0.001 (nm)
> WARNING no output, trajectory ended at 14
> However, if I issue the same trjconv command using "-dump 14" as shown 
> below, trjconv provides the correct snapshot at 14 ps:
> trjconv --f  traj.xtc -o  conf_pep.gro -s topol.tpr  -dump 14.0 
> But, this "-dump 14" command becomes extremely time consuming as I was 
> trying to get the snap-shot for a long time i.e around 30000ps . So, I 
> am trying to get "-b 14 -e 14" command work .    So, I was wondering 
> whether you have any clue how to get around with this.

If I recall, -b and -e cannot be the same.  This is the reason for -dump.  It 
might be worth a try to see if trjconv -b 13 -e 14 -dump 14 speeds things up any.


> Sanku


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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