Hi, 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? Regards, Tri
________________________________ From: [EMAIL PROTECTED] 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 Hi, 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. Solution: 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. Regards, Yang Ye ----- Original Message ---- From: #NGUYEN CONG TRI# <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <[email protected]> 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. Regards, Tri
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