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 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.
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