On 7/9/15 4:15 AM, PAULAMI CHATTERJEE wrote:
Dear All,
I have a 30 ns trajectory which I would like to extend up to 100 ns. For that I
gave the following commands
gmx convert-tpr -s md_0_1.tpr -extend 70000 -o final_monomer.tpr
gmx mdrun -s final_monomer.tpr -cpi md_0_1.cpt -append
After completion of the extension two new trajectory files were generated-
'traj.trr' and 'traj_comp.xtc' . When I tried to check the length of the
trajectory with
gmxcheck -f traj_comp.xtc
the output is
Checking file traj_comp.xtc
Reading frame 0 time 30000.000
# Atoms 16867
Precision 0.001 (nm)
Last frame 35000 time 100000.000
This trajectory file contains coordinate values from 30ns to 100ns. I tried to
calculate the rmsd with this file (both the trr and xtc file) but the graph
abruptly starts from 30ns (instead of 0) and continues upto 100ns.For the
calculation I need the total trajectory from time 0 to time 100ns.I think I am
missing something.
Indeed, you're missing your first trajectory.
You specified -append but if you're changing file names then that won't happen
and you need to use trjcat afterwards. But since you haven't told us what the
initial mdrun command was, there's no way to say what's going on for sure.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
[email protected] | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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