[gmx-users] Biphasic Systems for BSA

[Justin Lemkul]

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

-- 
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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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