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.
-Justin
Sanku
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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