Thanks for the advice ... I have checked all the equilibration graphs and they have converged well... I want to know one more thing about the anaylsis of simulation result.... I want to know whether the water molecules are entering in the protein molecule or not and if so how to track down those specific water molecules .. ( since I am simulating a GFP which is well protected from water and I have made some changes in the structure of GFP and then simulating it to see how this leads to change in protein structure ?? )
On Fri, Jan 28, 2011 at 5:00 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > sonali dhindwal wrote: > >> Hi Justin, >> >> I am writing in this correspondence, because I also had the same query >> once that secondary structure changes after equilibration, and you are right >> that visualisation programs are not always reliable. >> You also mentioned this time that we should check wether equilibration >> sufficiently converged all of the thermodynamic observables. It will be very >> kind of you if you can throw some light in this regard that how these >> observables should be checked. >> >> > Presumably, you've chosen an ensemble (NVT, NPT, etc) that represents some > set of desirable conditions. You have to make sure that properties like > temperature, pressure, density, energy, etc have converged, otherwise the > system is not yet equilibrated under those conditions. > > -Justin > > Thanks and Regards >> >> -- >> Sonali Dhindwal >> >> “Live as if you were to die tomorrow. Learn as if you were to live >> forever.” >> >> >> --- On *Fri, 28/1/11, Justin A. Lemkul /<jalem...@vt.edu>/* wrote: >> >> >> From: Justin A. Lemkul <jalem...@vt.edu> >> Subject: Re: [gmx-users] change in secondary structure after npt >> equilibration >> To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> >> Date: Friday, 28 January, 2011, 5:53 PM >> >> >> >> >> bharat gupta wrote: >> > Hi, >> > >> > >> > I am doing a simulation of a 230 amino acid protein for 3ns ... >> and I have completed the npt equilibration step .. After retrieving >> the structure from npt step and viewing it in pymol, reveals that >> some portion of the beta strand got changed to a loop but when I >> visualized the same structure in VMD I found that nothing has >> happened to the structure .. In order to confirm more ... I >> generated the SS profile using dssp and I found that , the dssp >> shows E i.e. sheet for that region .. So what shall i do next ... >> shall I continue with the production step or not ?? >> > >> >> Visualization programs are not always reliable in what they show >> you, we've discussed that. Methods like DSSP and STRIDE are far >> more trustworthy, and seem to indicate that your structure is fine. >> What you should be much more concerned with at this point is whether >> or not your equilibration sufficiently converged all of the >> thermodynamic observables. >> >> -Justin >> >> > -- Bharat >> > Ph.D. Candidate >> > Room No. : 7202A, 2nd Floor >> > Biomolecular Engineering Laboratory >> > Division of Chemical Engineering and Polymer Science >> > Pusan National University >> > Busan -609735 >> > South Korea >> > Lab phone no. - +82-51-510-3680, +82-51-583-8343 >> > >> > Mobile no. - 010-5818-3680 >> > E-mail : monu46...@yahoo.com </mc/compose?to=monu46...@yahoo.com> >> <mailto:monu46...@yahoo.com </mc/compose?to=monu46...@yahoo.com>> >> >> > >> >> -- ======================================== >> >> 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 >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> </mc/compose?to=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 >> </mc/compose?to=gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> > -- > ======================================== > > 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 > > ======================================== > -- > 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 > -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com
-- 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