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

James Starlight jmsstarlight at gmail.com
Sat Feb 4 17:27:43 CET 2012

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 ?

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 ?

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