[gmx-users] problem about rmsd

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 21 18:57:21 CET 2008

Quoting sudheer babu <sudheer.pbm07 at gmail.com>:

> Thanks for your reply,
> I am mentioning commands, from crashing the simulation
> 1. tpbconv  -f  protein.trr  -s protein.tpr -e protein.edr -n index.ndx -o
> out.tpr

You didn't tell tpbconv how long to continue the simulation.  Use tpbconv -until


> 2.mdrun -v -deffnm -o out.tpr
> 3.trjcat -f 633ps_pro.xtc 1ns_pro.xtc -settime -o
>   it asked time I mentioned  0 and 633, then it shown that 900ps trajectory
> files wirte into trjout.xtc
> 4.g_rms -f trjout.xtc -s em_wat.gro -pbc -o 1ns_rmsd
> 5. by using this plotted graph it shown values till 900ps on x-axis in
> gnuplot
> is there any way to get 1000ps simulation values?
> Thanks in advance.


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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