g_rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -n index.ndx -o rmsd.xvg -tu ps

(select parameters accordingly)

Hi Priyanka,

gmx rms let you determine the RMSD for your protein or complex, you have to select which case into all the options displayed when run gmx rms command. Additionally, you can perform different analyses for different groups of atoms by creating an index.ndx file with gmx make command.

gmx rms -s em.tpr -f traj.xtc -n index.ndx -o rmsd.xvg

See: http://manual.gromacs.org/archive/5.0/programs/gmx-rms.html

Hi,

1st you have to index group for protein and protein+ligand (complex)

gmx make_ndx -f xxx.gro -o protein/complex.ndx

2nd using gmx rms generate the rmsd using index file.

Hi, Priyanka Nath gmx rms -f *.xtc or trr -s *.tpr -tu ns