Dear justin http://rmsdnagasundaram.blogspot.in/. This is the link to my rmsd graph. Plz check it once and suggest me.
Thanks On Mon, Sep 24, 2012 at 10:10 PM, ahmet yıldırım <ahmedo...@gmail.com>wrote: > 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 > -- 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