Hi, RMSD's above 1 nm are suspect, towards 2 highly likely not correct. You have to make sure that the molecule is made whole before doing RMSD analysis.
Cheers, Tsjerk On Mon, Sep 24, 2012 at 3:02 PM, lloyd riggs <lloyd.ri...@gmx.ch> wrote: > 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Biocomputing Group Department of Biological Sciences 2500 University Drive NW Calgary, AB T2N 1N4 Canada -- 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