Fwd: [gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 17 07:47:01 CET 2012

On 17/02/2012 5:33 PM, James Starlight wrote:
> Mark,
> The pure Ccl4 cube was expanded in X dimension during npt phase.

So assuming you simulated long enough to have reasonable convergence, 
your model is not stable at the initial volume with whatever that 
reference pressure was.

> By the way I've been able to prevent it by increasing the ref_p of X 
> up to 5 ussing semiisotropic pcoupltype
> By when I've inserted peptide on the npt of that system my Ccl4 box 
> was expanded on Z rapidly.

It's likely a waste of time to insert stuff into a solvent system that 
is far from equilibrium.

> Might  this way to increase ref_p be usefull ?

Depends what you want to measure under what conditions.

> I want to obtain very tightly packet Ccl4 layer with high density 
> (~1500kg/m^3) to mimick membrane acyl-chain hydrophobic layer

So either you'll need high pressure or a different model of CCl4. Surely 
the work you are following addressed this. Your decision.


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