[gmx-users] water temperature 10 to 20 degrees higher than specified value

Moore, Jonathan (J) JMoore2 at dow.com
Mon Jun 6 23:02:59 CEST 2005

I'm reposting a couple questions since I didn't get any response the first times they were asked:

Question 1:
What could I be doing wrong?

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 <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.  

Question 2:
Could someone give an update on the status of implicit solvent capabilities in GROMACS?

As far as I can tell, the ever-popular "implicit solvent" question has been asked twice in 2005 on gmx-users without being answered:

http://www.gromacs.org/pipermail/gmx-users/2005-February/014029.html <http://www.gromacs.org/pipermail/gmx-users/2005-February/014029.html> 
http://www.gromacs.org/pipermail/gmx-users/2005-March/014644.html <http://www.gromacs.org/pipermail/gmx-users/2005-March/014644.html> 


Jonathan Moore, Ph.D.
Core R&D - New Products
The Dow Chemical Company
1702 Building, Office 4E
Midland, MI 48674  USA
Phone:  (989) 636-9765 
Fax: (989) 636-4019
E Mail: jmoore2 at dow.com

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