[gmx-users] Issue with RMSD for protein drug complex

[Sainitin Donakonda]

Hi all,

I ran 20ns simulation on protein drug complex..now i want to check overall
stability of this complex
to acheive this i did following i supplied index file and choose
Protein_Lig option for both least square fit and RMSD calculation..i used
following command

g_rms -f em.tpr (intital structure before production run) -s file.xtc (with
out pbc) -n index.ndx -o complex.xvg


is this correct way to determine overall stability of the complex ? or
should i use only back bone of protein?

Can any body let me know about it ?

Thanks in Advance

Sainitin