[gmx-users] Desired density - genbox

[Steven Neumann]

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?


Steven
 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
>
> --
> ========================================
>
> 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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