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.
On 5 October 2010 17:16, vinothkumar mohanakrishnan <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>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>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 >>> 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 >> >> >> -- >> 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 > -- Anil R.Mhashal Research fellow Physical Chemistry Division National Chemical Laboratory Pune
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