[gmx-users] Selecting part of the trajectory

#NGUYEN CONG TRI# NGUY0045 at ntu.edu.sg
Mon Oct 13 09:47:32 CEST 2008

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.
-------------- next part --------------
A non-text attachment was scrubbed...
Name: winmail.dat
Type: application/ms-tnef
Size: 3953 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20081013/d9cf3710/attachment.bin>

More information about the gromacs.org_gmx-users mailing list