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

[James Starlight]

Mark,

I've checked only density value

with 500 molecules Ccl4 I have  density that is twisely less that I need (
in accordance to the literature ). Also I've checked my box visually and
found that the box is not properly tightly packed so I dont know why genbox
didnt add some extra mollecules :(

In other words I wounder to know if  there is any way to add some extra
molecules to the pre defined box to make my system more tighly packed  ( to
short distance between existing molecules and place new ones in the new
space ) ?

James

2012/2/14 Mark Abraham <Mark.Abraham at anu.edu.au>

> 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
>
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