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 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
