[gmx-users] Themostat problem

[qiao rui]

Thanks, Anton.

I agree with what you are saying. I think perhaps another
way is not to couple the ions to the thermostat at all: since the ions are
immersed in the solvent whose temperature is maintained well, the thermal
fluctuation between ion and solvent should take care of the temperature
coupling nicely.

sincerely,

Rui

------------------------
Rui Qiao
Research Assistant
Beckman Institute, UIUC

On Thu, 23 Oct 2003, Anton Feenstra wrote:

> qiao rui wrote:
>
> > Dear All:
> >
> > 	I am trying to use Nose-Hoover thermostat for my simulation
> > system, where I have ~1500 water molecules, ~50 Na+ and ~50~ Cl- ions. I
> > used the following paramters:
> > 	tau_t = 0.05 ps; t_ref = 300K for each group.
> >
> > 	Using g_energy, I got the following statistics:
> >
> > Energy             Average       RMSD     Fluct.      Drift  Tot-Drift
> > -------------------------------------------------------------------------------
> > T-SOL              300       4.91058    4.90895 -0.000912265   -0.437889
> > T-Na               300.003   279.733    243.602   0.992376    476.343
> > T-Cl               299.997    385.632    373.082    0.70422    338.027
> >
> > 	It seems that the fluctuation of the temperature for Na+ and Cl-
> > is huge. Is there some way to solve the problem?
>
> Are you sure it is a problem? I'd imagine that for a small number (~50)
> of particles, temperature could fluctuate considerably, this is not
> necessarily a problem as long as the average is right (as it appears to
> be for your case). If these ions are free in the solvent, I would personally
> couple them together with the solvent to one bath, as heat exchange between
> water and solvated ions is relatively fast (i.e. you shouldn't see
> temperature differences building up between solvent and ions even when
> they're coupled as one).
>
> > 	Another question I have is: is it possible to just couple the x-
> > and y- degree of freedom with the themostat instead of coupling all the
> > three directions to the thermostat?
>
> In principle you could do that, but I don't see the point. THere is one
> problem that I see, is that you'd need to define kinetic energy and
> number of degrees of freedom in two dimensions in stead of three. It
> might be trivial, but I'm not sure... Also, I'm not familiar with the
> details of the nose-hoover thermostat, there may be caveats there as well...
>
>
> --
> Groetjes,
>
> Anton
>   _____________ _______________________________________________________
> |             |                                                       |
> |  _   _  ___,| K. Anton Feenstra                                     |
> | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
> |             | "If You See Me Getting High, Knock Me Down"           |
> |             | (Red Hot Chili Peppers)                               |
> |_____________|_______________________________________________________|
>
>
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