Dear Tsjerk, You said "RMSD's above 1 nm are suspect, towards 2 highly likely not correct." What is the physical/biological/chemical meaning of what you say?
Greetings 2012/9/24 Tsjerk Wassenaar <tsje...@gmail.com> > 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 > -- Ahmet Yıldırım -- 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
