[gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer
jmsstarlight at gmail.com
Tue Feb 14 07:17:14 CET 2012
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 ) ?
2012/2/14 Mark Abraham <Mark.Abraham at anu.edu.au>
> On 14/02/2012 4:57 PM, James Starlight wrote:
>> 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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