[gmx-users] water temperature 10 to 20 degrees higher than specified value
X.Periole at rug.nl
Tue Jun 7 08:46:15 CEST 2005
> 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> ). 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.
The problem might be the cut-off. You should be using a
twin-range cut-off, 0.8/1.4 nm, if you don't. Also
increasing the frequency of update of the lists should
help: use 5 steps.
> 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:
No implict solvent at this time in GROMACS.
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