[gmx-users] High temperature Simulation

[Daniel Adriano Silva M]

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 <bipinelmat at gmail.com>

> 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 <jalemkul at vt.edu> 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 <hmkvsri at gmail.com> 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
> >>>
> >>>
> >>> --
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> >>
> >>
> >>
> >
> > --
> > ========================================
> >
> > 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
> >
> > ========================================
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>
>
>
> --
> -----------------------
> Regards,
> Bipin Singh
> --
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