[gmx-users] Biphasic Systems for BSA

[Tsjerk Wassenaar]

Hi,

Actually no, you may be better off with a hexagonal prism, or even a
rhombic dodecahedron, which has a hexagonal base too.

Oh, and that structure of BSA is a dimer, while the biological unit is a
monomer...

Cheers,

Tsjerk
On Jun 27, 2015 7:20 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 6/27/15 2:38 AM, James Lord wrote:
>
>> Hi all,
>> I have a trivial question, What is the best box type and size for a big
>> protein such as BSA (attached .pdb) to minimize computational cost? what
>> is
>> the rule of thumb re the protein distance to box wall?
>> This protein is around 16 nm in x direction and 6nm in y.
>>
>> https://drive.google.com/file/d/0B0YMTXH1gmQsdGd2Z2xtVENzZkk/view?usp=sharing
>>
>>
> If, as your subject line implies, you are setting up a layered system, you
> are largely stuck with a rectangular box.  The dimensions can easily be
> determined by setting up the protein in a cubic box with editconf and
> conventional solute-box distances.  That distance depends on the force
> field (viz. the required cutoffs), to avoid minimum-image violations.  This
> is all very rudimentary stuff and is covered by tutorials and MD texts.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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