[gmx-users] Desired density - genbox

[Justin Lemkul]

On 3/18/13 6:14 PM, Steven Neumann wrote:
> On Mon, Mar 18, 2013 at 8:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> 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.
>
> Thanks.
> Larger box will need more molecules which is quite obvious so the same
> problem occurs. I need a cubic box first with given fixed density and
> then equilibrate it. Further step is to extend the box in one
> dimension to get properties I want.
> Shall manually add them then?
>

I think you missed the point of what I was saying.  You can use a larger box, 
with 850 molecules inserted, and equilbrate under NPT (using isotropic pressure 
coupling to guarantee the box stays cubic).  Provided the force field model 
produces the density you want, that's all you need to do.

-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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