[gmx-users] How to prevent box shrinking incessantly at x and y when doing membrane simulation using semiisotropic couple type?

Klniu email at klniu.com
Mon Jun 4 03:34:11 CEST 2012

Dear Chris

Thanks again for your reply.

On Sat, Jun 2, 2012 at 10:52 PM, Christopher Neale <
chris.neale at mail.utoronto.ca> wrote:

>  I suspect that you can find an equation to relate the surface tension to
> the ratio of the pressure along z to the pressure along xy that is required
> to maintain the unit cell of a semi-isotropic simulation approximately
> constant when you use the same compressibility in all dimensions.

Actually there is an equation to calculate surface tension by lateral
pressure and normal pressure.

[image: Inline image 1]

1/2 shows there are two interfaces. Lz is the lenth of box-z. Pn(Z) is
normal pressure. Pt(Z) is (press-x + press-y)/2.

But pressure must be gotten by correct simulation.

> You might even find an equation that was based on the rate of unit cell
> deformation when applying the same pressure in all dimensions. Since this
> is a non-equilibrium simulation you may need to run many of them to get an
> average rate.

Sorry I don't know how to contact the rate to the  surface tension. Or
should I use this rate to set my pressure or compressbility?

> Alternatively, you might consider simulating a spherical glob of decane in
> a water bath and finding equations that relate the aspherocity to the
> surface tension.

It's interesting and I am thinking about it. It needs a lot of work to do.

> If I were you, I'd look into physics textbooks to find some relation like
> this that you can use.
> Chris.
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