You can also just quickly visualize it in VMD and see if anything your looking at is not centred properly. If it isnt you just have to centre it.
Stephan -------- Original-Nachricht -------- > Datum: Mon, 24 Sep 2012 04:32:33 -0700 > Von: naga sundar <naga25sun...@gmail.com> > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > Betreff: Re: [gmx-users] Regarding RMSD analysis result > Dear justin > > Thanks for ur suggestions > > While speaking about periodic conditions, I followed > the similar condition for both native and mutant complexes. For native > complexes not any big deviation was observed. So its confirmed that > nothing > wrong with periodic conditions. Since all the three mutations were having > high clinical significance, we assuming mutation is the only reason for > this abnormal RMSD behavior. Sudden big increase in the RMSD was observed > in previous mutational MD studies. > http://www.sciencedirect.com/science/article/pii/S0006291X08020792. > > Overall, all the factors are supporting our results. So shall we take > this > RMSD analysis as good result . Even after repeating the 20 ns MD > simulation > two times i got the same results. > > > > > > > > > On Mon, Sep 24, 2012 at 3:41 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > On 9/24/12 6:24 AM, naga sundar wrote: > > > >> Dear gromacs users > >> > >> We performed MD simulation analysis for native and mutant > >> models of protein-protein complexes. From 20 ns simulation trajectory, > we > >> generated RMSD graph for one native and three mutant complexes. For > native > >> complex in the entire simulation period, we observed a constant RMSD > >> (~0.15 to ~ 0.25 nm). But, three mutant complexes > >> showed drastic fluctuation in theRMSD (~0.15 to ~1.75) plot. We > analysed > >> all the 3D structure's in the fluctuated areas observed destruction of > >> protein complexes. > >> All the three mutants were already experimentally analyzed and reported > >> that they are involved in the destruction of protein-protein > interactions. > >> > >> Query 1: What may be the reason for sudden rise and fall of the RMSD > >> values > >> in mutant complexes. We are assume its because of the involvement of > >> mutation. > >> Query 2: Is there may any other reasons for drastic fluctuation in the > >> RMSD > >> Query 3: Observed results are rite. > >> > >> Here iam attaching the RMSD graph for your observation. > >> > >> > >> > > Attachments to the list do not work. You will have to post a link to a > > file sharing site if you wish to share an image. > > > > Such jumps in RMSD are very suspect. Since you are dealing with > > protein-protein complexes, accounting for periodicity can be very > > challenging. Have you properly fit the trajectory such that your > protein > > subunits are not jumping across periodic boundaries? If they are, then > > your results are nothing more than an artifact. If they are not, then > you > > have something more interesting, but a tenfold increase in RMSD is very > > peculiar. > > > > -Justin > > > > -- > > ==============================**========== > > > > Justin A. Lemkul, Ph.D. > > Research Scientist > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > jalemkul[at]vt.edu | (540) 231-9080 > > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > > > ==============================**========== > > -- > > 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 -- 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
