I searched the user list .. I am not able to find how to apprach this problem .. I want to check whether water is entering the protein and interacting with chromophore or not ?? ...
On Fri, Jan 28, 2011 at 5:10 AM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > bharat gupta wrote: > >> 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 >> ?? ) >> >> > Watching the trajectory is the first step. There may be ways to quantify > these water molecules, using e.g. g_select or perhaps trjorder, but I can't > say that I actually know how to do that. I've never had to try :) > > -Justin > > On Fri, Jan 28, 2011 at 5:00 AM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> 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 >> <mailto:jalem...@vt.edu>>/* wrote: >> >> >> From: Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>> >> >> >> Subject: Re: [gmx-users] change in secondary structure after npt >> equilibration >> To: "Discussion list for GROMACS users" >> <gmx-users@gromacs.org <mailto: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> >> </mc/compose?to=monu46...@yahoo.com <mailto:monu46...@yahoo.com>> >> <mailto:monu46...@yahoo.com <mailto:monu46...@yahoo.com> >> </mc/compose?to=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 <http://vt.edu/> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> </mc/compose?to=gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org> >> >> </mc/compose?to=gmx-users-requ...@gromacs.org >> <mailto: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 <http://vt.edu/> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto: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 <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 > -- 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
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