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

Mark Abraham Mark.Abraham at anu.edu.au
Tue Feb 14 07:02:43 CET 2012

On 14/02/2012 4:57 PM, James Starlight wrote:
> Justin,
> Firstly I've created the box of desired size with only 500 molecules ( 
> I need 1000)
> Than I've tried to add extra 200 molecules by means of Genbox
> genbox -cp super_box.gro -ci Ccl4.gro -nmol 200 -o new_solv.gro
> but no molecules have been added
> Added 0 molecules (out of 200 requested) of Cl4

... then there are no gaps large enough to insert your molecules. Either 
make gaps, or check out genbox -h for advice on defining the radii.

> also I've tried
> genbox -cp super_box.gro -cp Ccl4.gro -nmol 200 -o new_solv.gro

Two -cp options is not what you want, and -nmol probably only works with 

> but system were crashed with message
> Reading solute configuration
> God Rules Over Mankind, Animals, Cosmos and Such
> Containing 2500 atoms in 500 residues
> Initialising van der waals distances...
> WARNING: masses and atomic (Van der Waals) radii will be determined
>          based on residue and atom names. These numbers can deviate
>          from the correct mass and radius of the atom type.
> Reading solvent configuration
> "God Rules Over Mankind, Animals, Cosmos and Such"
> solvent configuration contains 5 atoms in 1 residues
> Is there any ways to add extra mollecules to the pre defined box ?

Yes - but there has to be room for them.


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