[gmx-users] Selecting part of the trajectory

[#NGUYEN CONG TRI#]

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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