[gmx-users] regarding box dimension and number of solvent molecules

[Mark Abraham]

On 23/01/2012 9:27 PM, priya thiyagarajan wrote:
> hello sir,
>
> i like to know few informations regarding box dimension and setting 
> no.of.solvent molecules..
>
> i want to run simulation for different number of protein molecules 
> with same number of water molecules..
>  i used following commands
> to increase the no.of molecules i used
> genbox -nmol 100 -ci protein.pdb -box 15 15 15 -o protein100.pdb
>
> then i set box type
>
> editconf -f protein100.pdb -bt cubic -o prot100_box.pdb -box 15 15 15
>
> to add water
>
>
> genbox -cp prot100_box.pdb -cs spc216.gro -p topol.top -o 
> prot100_water.pdb  -maxsol 50000
>
>
>
> when i added  50000 water molecules only half of my box is getting 
> filled by solvent molecules..
>

Go and work out how many water molecules at normal density you can have 
in a 15nm^3 box.

Mark
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