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

[Mark Abraham]

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 
-ci.

>
> 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.

Mark