[gmx-users] How to keep my box from exploding...

[Erik Lindahl]

Hi Chris,


On Thursday, Apr 24, 2003, at 14:48 US/Pacific, curtchr1 at iit.edu wrote:

> I am currently trying to run a simulation in which I have four groups  
> with
> the following conditions:
>
> temperature coupling = berendsen
> ref-t = 5 5 5 5
> tau-t = .1 .1 .1 .1
>

This doesn't affect the pressure, but I hope you're aware that you are  
coupling the temperature to 5K :-)

> pressure coupling = berendsen
> ref-p = 1.0 1.0 1.0 1.0
> compressibility = 4e-5 4e-5 4e-5 4e-5
> tau-p = .1 .1 .1 .1
>


0.1 ps is an extremely short time constant for the pressure scaling,  
that's why you are getting oscillations.

Try values in the 1-20ps range instead!

Cheers,

Erik

>
------------------------------------------------------------------------ 
-----
Erik Lindahl, MSc, PhD     <lindahl at stanford.edu>
D109, Fairchild Building
Dept. Structural Biology, Stanford University School of Medicine
Tel. 650-7250754    Fax. 650-7238464