[gmx-users] Desired density - genbox

[Justin Lemkul]

On 3/19/13 5:52 AM, Steven Neumann wrote:
> 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?
>

If the force field has been parametrized to reproduce the density, then yes.

-Justin

> 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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-- 
========================================

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

========================================