Thanks Tsjerk Can you plz tell me How do we really conclude that an biologically relevant motion or a simple relaxation ( i have followed this approach, i also carried out a elastic netwok modelling based PCA and comapred the lowest mode obtained from EN-NMA with my PC1- Is this a right approach??)
Thanks Regards Vijayan.R On Wed, Dec 21, 2011 at 10:51 AM, Tsjerk Wassenaar <tsje...@gmail.com>wrote: > Hi Vijayan R., > > Eigenvectors are specific up to a sign. So it's not said the start will > end up as the negative extreme. It seems your interpolation just shows what > happens in reverse. > As a sidenote, do check whether it is a biologically relevant motion, or > merely relaxation. > > Cheers, > > Tsjerk > > On Dec 21, 2011 4:24 PM, "R.S.K.Vijayan" <biovija...@gmail.com> wrote: > > > Hi all > > I carried out a distance analysis between two domains with respect to > time based on the center of mass. Subsequently i also carried out a PCA > based essential dynamics to identify the global/biologically relevant > motions. The strange and inconsistent result i find here is > > when i calculate the distance using the MD (progressive fitted) > trajectory, I find that the two domains of interest move apart with respect > to time. > > on the contrary a ED followed by a smoothed interpolation between the two > extreme motions revelas that the two domains move closer to each other in a > concerted fashion. > > does any one has an explanation for this discrepancy between ED motions > and the MD motion ??? > > Thanking you in advance > > Regards > Vijayan.R > > > > On Tue, Dec 20, 2011 at 2:28 AM, bipin singh <bipinel...@gmail.com> wrote: > >> Thanks a lot for your suggestions. >> >> On Mon, Dec 19, 2011 at 21:00, David Mobley <dmob...@gmail.com> wrote: >> >>> Yes, changing the net charge of the system is something that is rather >>> complicated in fact (one can plunge ahead and do it while ignoring the >>> complications, but the results will typically be rather system-size >>> dependent and essentially wrong). For more details refer to the Kastenholz >>> and Hunenberger papers from J. Chem. Phys (2006 or 2007) and references >>> therein. The good news is that for simple spherical ions K&H have worked >>> out the relevant corrections. The bad news is that if you move away from >>> simple spherical ions you've got problems. >>> >>> David Mobley >>> >>> >>> >>> On Fri, Dec 16, 2011 at 6:41 AM, Justin A. Lemkul <jalem...@vt.edu>wrote: >>> >>>> >>>> >>>> bipin singh wrote: >>>> >>>>> Hello, >>>>> >>>>> I am willing to study the free energy of binding of a cation (Ca++) to >>>>> the protein and I am following the free energy tutorial >>>>> provided by Justin >>>>> (http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin/** >>>>> gmx-tutorials/free_energy<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy> >>>>> ). >>>>> Please let me know whether the settings for this type of study would >>>>> be same as given in the tutorial for ligand-Protein >>>>> binding free energy calculation or it need some different approach: >>>>> >>>> >>>> By decoupling a Ca2+ ion, you are removing 2 charges from the system. >>>> I don't know how to properly treat such a case (perhaps someone else can >>>> comment), but likely you'll find such topics in the literature. A better >>>> approach may be umbrella sampling, but again the literature should point >>>> you to reasonable methodology. I'm sure others have dealt with such >>>> questions before. >>>> >>>> -Justin >>>> >>>> >>>> The setting from the ligand-Protein binding free energy calculation >>>>> are given as: >>>>> >>>>> >>>>> van der Waals coupling: >>>>> >>>>> sc-alpha = 0.5 ; use soft-core for LJ (de)coupling >>>>> sc-sigma = 0.3 >>>>> sc-power = 1 >>>>> couple-moltype = LIG >>>>> couple-intramol = no >>>>> couple-lambda0 = none ; non-interacting dummy in state A >>>>> couple-lambda1 = vdw ; only vdW terms on in state B >>>>> >>>>> Coulombic coupling: >>>>> >>>>> sc-alpha = 0 ; soft-core during (dis)charging can >>>>> be unstable! >>>>> sc-sigma = 0 >>>>> couple-moltype = LIG >>>>> couple-intramol = no >>>>> couple-lambda0 = vdw ; only vdW terms in state A (the >>>>> previous state B is now A) >>>>> couple-lambda1 = vdw-q ; all nonbonded interactions are on in >>>>> state B >>>>> >>>>> >>>>> >>>> -- >>>> ==============================**========== >>>> >>>> Justin A. Lemkul >>>> Ph.D. Candidate >>>> ICTAS Doctoral Scholar >>>> MILES-IGERT Trainee >>>> 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> >>>> >>> >>> >>> >>> -- >>> David Mobley >>> dmob...@gmail.com >>> 504-383-3662 >>> >>> >>> >>> -- >>> 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,* >> Bipin Singh >> >> >> -- >> 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 > > > -- > 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 >
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