[gmx-users] trjconv problem

Sanku M msanku65 at yahoo.com
Thu May 5 17:33:19 CEST 2011

Hi Justin,
  In many of the frames, if I use -b and -e to be same , it works
For example, I found if I use -b 16 -e 16, it gives me the the snapshot at 16ps. 
 But, in many cases like 14ps, it is not working. Also, I tried -b 13 -e 14 
-dump 14  . It does not work saying 'WARNING no output, trajectory ended at 14'
Any help will be appreciated.

From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Thu, May 5, 2011 10:22:38 AM
Subject: Re: [gmx-users] trjconv problem

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 


> 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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