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

Justin A. Lemkul jalemkul at vt.edu
Sat Feb 4 17:33:56 CET 2012

James Starlight wrote:
> Dear Gromacs Users!
> I have problems during npt equilibration of my solvent box with the CCl4 
> solvent (I'm preparing this hydrophobic layer for further 
> membrane-mimicking system).
> As the result I want to obtain density value ~ 1.5 for such box but 
> between 2 and 3  ns ( where the desity was 1.3) of such simulation I've 
> obtain error
> 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.
> 1) What should I do in that case ? Should I use larger cutoofs ( I'm 
> using 0.9 nm with the Gromos 56 parameters ) or extend some box vectors ?

Larger cutoffs would not only make the problem worse (read the error message 
carefully and consider the minimum image convention), but it would also 
potentially break the validity of the force field model.  The vdW cutoff for 
Gromos96 should be 1.4 nm, not 0.9 nm, in any case.

> 2) Initially I've tried to use membrane mimicking dimensions 8.6   6.5   
> 3.0 but during equilibration my box was shrinked to the 8.0 6.0 2.0
> How I could present such shrinking ?

You don't.  This is a normal consequence of a box that was too diffuse 
condensing to adopt the density that the force field model will produce.  It's 
probably best to start with a box that is more densely packed (closer to the 
target, to minimize shrinking).



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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