[gmx-users] High temperature Simulation

[Justin A. Lemkul]

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 <bipinelmat at gmail.com 
> <mailto:bipinelmat at gmail.com>> 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 <hmkvsri at gmail.com
>     <mailto: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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> 
> 
>     --
>     -----------------------
>     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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