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.
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 <mailto: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 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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