On 17/10/2011 10:58 PM, bipin singh wrote:
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.
There's still an energy, and we can compute its gradient with respect to
atomic coordinates, i.e. forces. EM algorithms move the atoms according
to those forces to see a stationary point on the potential energy
surface. MD algorithms use the forces to update velocities and
positions, integrating Newton's second law with a finite time step.
Mark
On Mon, Oct 17, 2011 at 17:03, Justin A. Lemkul<jalem...@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<hmkv...@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
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jalemkul[at]vt.edu | (540) 231-9080
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