[gmx-users] temperature

[Itamar Kass]

Hi Shahab,

The best temperature to use is 298K as this is the temperature in which
the force filed was parameterised. But, and this is a big but, I
speculate that any errors you might have during the simulation due to
the use of 310K is minimal and less then other inaccuracies in the force
field.

Best,
Itamar

-- 


"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut

===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at med.monash.edu.au
============================================

----- Original Message -----
From: shahab shariati <shahab.shariati at gmail.com>
Date: Tuesday, February 23, 2010 9:45 pm
Subject: [gmx-users] temperature
To: gmx-users at gromacs.org

> Hi gromacs users
> 
> I want to run simulation of protein-dna interaction.
> 
> what is best for temperature in mdp file: 1) 300K (default) 2) 310k
> (physiologic temperature)
> 
> 
> Any help will highly appreciated!
> 
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