Dear Felipe Thanks for ur reply.
The system is a protein-protein complex. Like u r saying its due to pbc problem then why any abnormality doesn't happened to the native complex (Black line)?. As already suggest by justin i checked the pbc conditions upto my knowledge everything is fine. of-course this is not the first MD run for these native and mutant complexes. I run twice and got the same results. I want know this kind of RMSD is rite r wrong?.. On Tue, Sep 25, 2012 at 12:45 AM, Felipe Pineda, PhD < luis.pinedadecas...@lnu.se> wrote: > It looks for me like the known pbc effect others already pointed to. If > you have just a protein-ligand complex (+ water and counterions of course) > it's relatively easy to manually (a piece of code would do it) bring the > ligand to the correct position in the frames showing an abnormally high > value by subtracting half the x/y dimension of the box from its coordinates > and re-calculate the rmsd , but I think trjconv would do it as well. > > Felipe > > > On 09/25/2012 09:22 AM, naga sundar wrote: > >> Dear justin >> >> >> http://rmsdnagasundaram.**blogspot.in/<http://rmsdnagasundaram.blogspot.in/>. >> This is the link to >> my rmsd graph. Plz check it once and suggest me. >> >> >> Thanks >> >> > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- Regards N.NagaSundaram -- 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