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
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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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