RMSD calculation error

User discussions
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1

GROMACS version: 2019
GROMACS modification: Yes/No
Hi All,

My system contains protein, ligand and nowater. I want to calculate RMSD after simulation and i have used commands.

gmx trjconv -s md_1.tpr -f md_1.xtc -o traj_1.xtc -pbc nojump
gmx rms -s md_1.tpr -f traj_1.xtc -o rmsd_noH_1.xvg -n Pro_MOL_noH.ndx -tu ns

After i run commands then program warms an error like that

rmsd
rmsd1074×276 91.1 KB

Appreciate your help in fixing this.

Thank you.

Best regards
Hang NT Nguyen

2

what is included in the index (.ndx*) file?Try to calculate RMSD of only protein (or C-alpha atoms) and save the first frame of the trajectory as your reference.