GROMACS version: 2024.2
GROMACS modification: No
Hello everyone,
I performed a 100 ns MD simulation on a protein ligand complex and my output files are named: md_0_100.cpt and md_0_100.xtc. I decided to extend it to 200 ns and created a new tpr file named md_1_100.tpr with grompp (maybe I should have used convert-tpr). And then, I used :
“gmx mdrun -deffnm md_1_100 -cpi md_0_100.cpt -nb gpu -noappend”. This way I get the second trajectory file and renamed it to md_1_100.xtc (erased part0002).
After that i concatenated trajectories with “gmx trjcat -f md_0_100.xtc md_1_100.xtc -o full_200.xtc -settime”. I choosed “0” for the first trajectory and “l” for the second and get full_200.xtc.
Now I want to calculate RMSD for this 200 ns trajectory. I need to do centering and fitting with this commands:
gmx trjconv -s md_1_100.tpr -f full_200.xtc -o full_200_center.xtc -center -pbc mol -ur compact -n index.ndx
gmx trjconv -s md_1_100.tpr -f full_200_center.xtc -o full_200_fit.xtc -fit rot+trans -n index.ndx
Then I calculated RMSD of backbone-ligand and RMSD values are between 10-11 nm. But my RMSD values were between 0.4-0.5 nm for first 100 ns trajectory. I think I made something wrong on exteded run step and centering and fitting after that. Any help would be appreciated and sorry for the long post.