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

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 10 13:59:35 CET 2012

James Starlight wrote:
> Justin, 
> 2012/2/6 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>     Some simple calculations using the desired density and the box
>     dimensions (to get the volume) will tell you exactly how many
>     molecules you need.  If you only "suppose" you've got a reasonable
>     number, there are better ways to be sure ;)
> In accordance to my calculations I need in ~ 1000 CCl4 to obtain 1.600 
> g/cm^-3 density with my box dimensins
> By the way way I try to define such system by
> genbox -ci ccl4.gro -nmol 1000 -box 8.6 6.5 3 -o ccl4_box.gro
> I've obtain memory error :(
> Is there any other way to define such system with the desired size and n_mollecules with the less computation demands?

Two options:

1. Add them incrementally to the box (100 at a time or so, until the desired 
value is reached)

2. Build a small box of solvent (a few hundred molecules), then use genbox -cs 
instead of -ci to use the small solvent box to create the one of desired size.



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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