[gmx-users] problem about rmsd

Mark Abraham Mark.Abraham at anu.edu.au
Sat Mar 22 01:20:56 CET 2008

sudheer babu wrote:
> 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

Look closely at the output here, and your original nstvout .mdp value. 
Unless you wrote velocities every picosecond, you won't be able to 
restart from 633ps, and tpbconv will have complained about incomplete 
frames. tpbconv will have told you what it compromised, so read it 
carefully. Also, read http://wiki.gromacs.org/index.php/Doing_Restarts 

> 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

Use gmxcheck on the two trajectories to see what you actually have.

> 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.
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