Yeah... A equilibration can be complish within the ps n we have to make ensure that the there should not be more fluctuation in the potential energy in other words it should be stabilize.
On 5 October 2010 17:47, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Anil Mhashal wrote: > >> Just plot a graph of the potential energy with respect to the time and >> check the energy fluctuation, it should be less than 10% of the average >> potential energy then u can say that ur protein is equilibrated. >> >> > I would think that, for most systems, a fluctuation of 10% is quite large. > I would expect most stable systems to fluctuate less than 1%, if that. > Even then, you can judge very little from potential energy alone. The > simulation may be stable at that point, but without more analysis, I'd say > it is hard to judge how equilibrated the system is. In my experience, the > potential energy generally converges within a few ps, but other properties > may take substantially longer to converge. > > -Justin > > >> On 5 October 2010 17:16, vinothkumar mohanakrishnan >> <kmvin...@gmail.com<mailto: >> kmvin...@gmail.com>> wrote: >> >> hi anil >> >> i get the potential energy at the end of the mdrun. if i want to >> calulate the deviation with what i should compare and calculate the >> deviation.can you be more specific. >> >> Regards >> Vinoth >> >> >> On Tue, Oct 5, 2010 at 4:51 PM, Anil Mhashal >> <anil2000.2...@gmail.com <mailto:anil2000.2...@gmail.com>> wrote: >> >> To check ur equilibration, just look at the potential energy >> and find out the deviation in the energy if the deviation in the >> energy is within 10% then ur equilibration is successful... >> >> On 5 October 2010 14:56, vinothkumar mohanakrishnan >> <kmvin...@gmail.com <mailto:kmvin...@gmail.com>> wrote: >> >> Hi all >> >> Suppose say i have a box of decane molecules and i want to >> equilibrate. say i have all the necessary files to run >> mdrun. on what basis i say whether my equilibration is >> successful r not after the mdrun. what properties i should >> measure to know whether my equilibration was successful. >> >> Regards >> Vinoth >> >> -- >> >> 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 >> >> >> >> >> -- Anil R.Mhashal >> Research fellow >> Physical Chemistry Division >> National Chemical Laboratory >> Pune >> >> -- >> 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 >> >> >> >> -- >> 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 >> >> >> >> >> -- >> Anil R.Mhashal >> Research fellow >> Physical Chemistry Division >> National Chemical Laboratory >> Pune >> > > -- > ======================================== > > 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 > -- Anil R.Mhashal Research fellow Physical Chemistry Division National Chemical Laboratory Pune
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