minnale wrote:
Hi all,
I intersted in analysing secondary structure of protein by using VMD
and performed these steps.
1. First loaded min.gro file and corresponding min.xtc then all
equalibration .xtc files till here MD movie has run fine.
2. I had long trajectory in a single file, so cut it down into
subtrajectories with 1ns interval by using *trjconv command and issued
like this
trjconv -f .xtc -o 1ns.xtc -s .tpr -b 0 -e 1000
selected system, it showed
Fatal error:
Index[2725] 2726 is larger than the number of atoms in the trajectory
file (2725)
You've only saved a subset of your trajectory. Check the xtc-grps in your .mdp
file. You can use trjconv if you have a reference structure that matches the
contents of your trajectory.
-Justin
Could you please give me suggestion if any one have experienced this
type of problem
Thanks in advance.
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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