# Calculating RMSD from an extended run

**URL:** <https://gromacs.bioexcel.eu/t/calculating-rmsd-from-an-extended-run/12043>\
**Category:** User discussions\
**Created:** [May 7, 2025, 8:46am UTC](https://gromacs.bioexcel.eu/t/calculating-rmsd-from-an-extended-run/12043 "2025-05-07T08:46:47Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![ssari](https://avatars.discourse-cdn.com/v4/letter/s/35a633/32.png) [@ssari](https://gromacs.bioexcel.eu/u/ssari)\
**Post date:** [May 7, 2025, 8:46am UTC](https://gromacs.bioexcel.eu/t/calculating-rmsd-from-an-extended-run/12043/1 "2025-05-07T08:46:47Z")

</div>

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.