<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman, new york, times, serif;font-size:12pt">Hi,<div><br></div><div>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.</div><div><br></div><div>Solution:</div><div>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.</div><div> </div><div>Regards,<br>Yang Ye<div><br></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:10pt">----- Original Message ----<br>From: #NGUYEN CONG TRI# <NGUY0045@ntu.edu.sg><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Sent: Monday, October 13, 2008 3:47:32 PM<br>Subject: [gmx-users]
Selecting part of the trajectory<br><br>
Hi all,<br> <br>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:<br> <br>Fatal error:<br>Specified frame doesn't exist or file not seekable<br> <br>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.<br> <br>Thank you for any suggestion.<br> <br>Regards,<br>Tri<br></div></div><div
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