Kavyashree M wrote:
Thank you,
What about the pressure that need to be used at that temperature
(for a system of a protein in tip4p water)
The set pressure should reflect whatever system you are trying to model.
-Justin
Thank you
With Regards
Kavya
On Mon, Oct 17, 2011 at 3:29 PM, bipin singh <[email protected]
<mailto:[email protected]>> wrote:
As far as I know we do energy minimization at room temperature only.
Only during equilibration
(NVT and NPT) we use high temperature for maintaining proper density
before starting the final production run.
On Mon, Oct 17, 2011 at 15:15, Kavyashree M <[email protected]
<mailto:[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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Regards,
Bipin Singh
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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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