[gmx-users] Desired density - genbox

[Justin Lemkul]

On 3/18/13 2:56 PM, Steven Neumann wrote:
> Dear Gmx Users,
>
> I am trying to obtain given density for my system for a given molecule
> - its a cubic box of 5 nm in dimension.
>
> I calculated that I need 850 molecules to get the density of 500 g/mol
> In my box there is already 1 molecule so I try:
>
> genbox -cp Box.pdb -ci molecule.pdb -nmol 849 -o BoxMol.pdb
>
>
>
> Added 819 molecules (out of 849 requested)
> Output configuration contains 9020 atoms in 820 residues
> Volume                 :         125 (nm^3)
> Density                :     480.336 (g/l)
> Number of SOL molecules:      0
>
> How can I add 30 more molecules using gromacs? I want to avoid adding
> it manually.
>

Use a larger box and equilibrate.  All genbox tries to do is add molecules 
randomly, which is not a foolproof process.  If the force field parameters 
indeed produce the correct density, you should be able to produce it rather quickly.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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