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

Mark Abraham Mark.Abraham at anu.edu.au
Fri Feb 17 06:57:02 CET 2012

On 17/02/2012 4:46 PM, James Starlight wrote:
> So my problem still is
> 1) During npt without peptide my Ccl4 system expan rapidly in 
> X-dimension. That produce error on 2nd ns of equilibration
> One of the box vectors has become shorter than twice the cut-off 
> length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.
> 2) During npt with peptide my system expan rapidly in Z direction ( 
> along that axe my peptide is oriented) So as concequence I've obtained 
> the same error.

What does a cube of CCl4 do? If it is not stable at an acceptable 
density then your parameters don't work at all. Starting with simple 
things and adding complexity gradually is always a good policy, even 
when you're an expert. There's so many things that can be slightly wrong...

> Possible sollution wich I've found in litterature
> 1) To fix one dimension of my PB. How I could fix the X dimension of 
> my box during npt phace of pure Ccl4 and allow only change in 2 other 
> dimensions ?

See pcoupltype in manual 7.3.15

> 2) I have not found radius for Cl for Gromos56 ff.
> Is this possible to decrease that value during npt phase to obtain 
> system with desired hight density? What value should I use?

As someone else said, the radius is only material during things like 
genbox. In the simulation, your nonbonded parameters are the important 


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