[gmx-users] Desired density - genbox

[Steven Neumann]

Thanks. So in this case no matter what density I will start with e.g.
480 kg/m3 presuming the force filed is correct I should get at given
conditions the density of interest?

Steven

On Mon, Mar 18, 2013 at 10:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> --
> ========================================
>
> 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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