In the energy minimisation step, any "conformational rearrangement" taking place is not a function of time, it is just an algorithm for reaching a basin of minimum energy:
(http://www.gromacs.org/Documentation/Terminology/Energy_Minimisation), hence there are not velocities in the atoms of the system, and macroscopic properties related to dynamics (like temperature) are not present. Daniel Silva 2011/10/17 bipin singh <[email protected]> > I have not understood what you mean by > "Energy minimization is (theoretically) at 0 K, as there are no velocities > and it is not a true dynamical process." > It is clear to me that at 0K there would be no velocities but then why > during minimization we expect > some conformational rearrangement of side chains etc. > > > On Mon, Oct 17, 2011 at 17:03, Justin A. Lemkul <[email protected]> wrote: > > > > > > bipin singh wrote: > >> > >> As far as I know we do energy minimization at room temperature only. > > > > Energy minimization is (theoretically) at 0 K, as there are no velocities > > and it is not a true dynamical process. > > > >> Only during equilibration > >> (NVT and NPT) we use high temperature for maintaining proper density > >> before starting the final production run. > >> > > > > Maintaining density is but one possible goal for NPT; defining the > desired > > ensemble and therefore the sampling distribution is the main reason. > > > > -Justin > > > >> On Mon, Oct 17, 2011 at 15:15, Kavyashree M <[email protected]> wrote: > >>> > >>> Dear users, > >>> > >>> For simulating a protein at high temperature (more than 300K, > >>> less than 400K) using OPLSAA forcefield, what are the parameters > >>> other than Temperature that need to be taken care of? > >>> Does the energy minimization step also needs to be done at high > >>> temperature? (here my aim is not to simulate an unfolding event) > >>> I have a reference - > >>> Biophysical Journal Volume 94 June 2008 4444–4453 > >>> > >>> Any other references or suggestions will be helpful. > >>> > >>> Thanking you > >>> With Regards > >>> M. Kavyashree > >>> > >>> > >>> -- > >>> gmx-users mailing list [email protected] > >>> 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 [email protected]. > >>> 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 [email protected] > > 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 [email protected]. > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > -- > ----------------------- > Regards, > Bipin Singh > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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