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
carefully.
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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