[gmx-users] Compressibility issue - real concern

[Jones de Andrade]

Hi Erik.

I was thinking something about it exactly now. I mean, Berk quoted that the
scalling goes with beta/tau in Berendsen, and with beta/tay^2 in Parrinello.
I mean, in a similar implementation, how should it go for a nosè
implementation?

Also, what would be a good value for tau_p so? I was looking in, for
exemple, the "spider tutorial", and there they use a tau_p value of .5, not
so different from my value of .4 (and not .1).

Finally: it also mean that if I choose a beta and tau_p pair which yelds a
too low value, it won't really affect the equilibrium density of the system,
correct?

Thanks a lot in advance!

Sincerally yours,

Jones

On 5/3/07, Erik Lindahl <lindahl at cbr.su.se> wrote:
>
> Hi,
> On May 3, 2007, at 12:37 PM, Jones de Andrade wrote:
>
> Hi Berk! Thanks for your so fast answer!
>
> I'll try to look for a different tau_p. I would really feel 4 ps a too
> high value, even for water systems, but will look around before decision.
> Anyway, I'm still concerned about the compressibility value.
>
> Long time ago in this list I came to this question, and this is how this
> ended:
>
> **>* Hi,
> *>*
> *>* Just use the water value for any liquid system (5e-5 or so).
> *>
> *
> *>* As the manual explains, it only affects the coupling time, not the
> *>* equilibrium pressure.
> *>
>
>
> This is valid for long times, and (as always for pressure) assumes the
> external coupling to be clearly slower than the internal dynamics. I have no
> idea how Amber or DLPOLY sets their tau_t with Nose or Parinello-Rahman, but
> as specified in the Gromacs manual we use the period of average fluctuations
> at equilibrium. With tau=0.1 the system will very likely never reach that
> equilibrium.
>
> Cheers,
>
> Erik
>
>
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