[gmx-users] Biphasic Systems for BSA

[James Lord]

Hi Justin & Tsjerk,
Thanks for the info,
Tsjerk: I was looking for the monomer but could not find monomer structure
on protein data bank.
Cheers
James

On Sun, Jun 28, 2015 at 6:50 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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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