[gmx-users] System temperature

[Moore, Jonathan (J)]

I'm simulating cellulose (oligomer of nine rings) in water using 1.4 nm cut-off, Reaction Field, and LINCS bond-constraints (generally trying to follow the recipe used by H. Yu, M. Amann, T. Hansson, J. Köhler, G. Wich and W. F. van Gunsteren. "Effect of methylation on the stability and solvation free energy of amylose and cellulose fragments: a molecular dynamics study." Carbohydr. Res., 339, 1697-1709 (2004). http://dx.doi.org/10.1016/j.carres.2004.05.003).  The cellulose and water are separately coupled to a Berendsen thermostat with tau_t of 0.1.  The system contains one cellulose oligomer (129 atoms) and something like 16000 water molecules.  I'm simulating at various temperatures in the range of 283 to 363 K.  The cellulose is always close to the specified temperature but the water temperature is always higher by some 10 to 20 degrees.  True, I'm not using PME, but this large discrepancy seems unacceptable to me.  

What could I be doing wrong?


Thanks,
Jonathan

____________________________
Jonathan Moore, Ph.D.
Core R&D - New Products
The Dow Chemical Company
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-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel
Sent: Tuesday, May 31, 2005 5:45 AM
To: SemteX; Discussion list for GROMACS users
Subject: Re: [gmx-users] System temperature


On Tue, 2005-05-31 at 11:54 +0300, Arturas wrote:
> Hello,
> 
> I noticed that some MD simulations fluctuates about 302-305 °K, 
> although I defined 300 in mdp. I use 0.1 for temperature coupling.
> 
> This value is not so drastically odd, but why ? Is tau_t too large ?
This is due to using a cut-off, which systematically heats the system. If you use PME it will be within 0.5 K.

> 
> With best
> Arturas
> 
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-- 
David. ________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University.
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