[gmx-users] Selecting part of the trajectory

#NGUYEN CONG TRI# NGUY0045 at ntu.edu.sg
Tue Oct 14 09:34:12 CEST 2008

Thank you very much for your reply. No matter how much I much it backward, even with -b 100 and -e 200 it still doesn't work. And it's not just applied for 1 trajectory, I have 3 others as well but none seems to work. 
But I'm able to get the snapshots using -dump flag. Of course it's much slower because each time trjconv has to go through the whole 19ns again. Is it some problem inherent to the .xtc format itself that I cannot use -b and -e flags of trjconv?


From: gmx-users-bounces at gromacs.org on behalf of Yang Ye
Sent: Mon 10/13/2008 10:10 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Selecting part of the trajectory


This is a common problem to long trajectory. It is fine as long as there is no real corruption in the trajectory file, caused by network, disk, etc.

Shift a bit backward from the -b, this may be a few hundred ps or several ns, then extract the segment you would like to have from this secondary trajectory.
Yang Ye 

----- Original Message ----
From: #NGUYEN CONG TRI# <NGUY0045 at ntu.edu.sg>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Monday, October 13, 2008 3:47:32 PM
Subject: [gmx-users] Selecting part of the trajectory

Hi all,

I want get the snapshots every 5ps of the last 1ns in a 20 ns simulation. So I want to cut out the last 1ns. I was able to do that using -b and -e flags of trjconv, say -b 19000 and -e 20000 for a .trr trajectory. However, to save disk space I converted it into .xtc format and I cannot use trjconv with -b and -e flags anymore. I got error msg like:

Fatal error:
Specified frame doesn't exist or file not seekable

One more thing, my system consists of a protein and a ligand. At some snapshots, the ligand just jumps out of the box even when I used -pbc mol -ur compact. I tried with -pbc nojump and other option as well but none works perfectly in all cases. How to make sure that the ligand always stays with the protein so that I can write the script to automatically generate the snapshots and do some post-processing on them.

Thank you for any suggestion.


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