[gmx-users] macromolecule in solution

David spoel at xray.bmc.uu.se
Tue Sep 13 17:25:08 CEST 2005

On Tue, 2005-09-13 at 11:10 -0400, ARGYRIOS KARATRANTOS wrote:
> for a macromolecule in solution do I have to use exactly what gromacs says, that
> in any direction of the box, the box size must be: size of macromolecule +
> 2*Rcutoff?
> if I applied that in a long macromolecule chain I can not have the desirable
> mass fraction (Wpolymer=0.2)

You decide, you have to defend your choices to the referee of your
paper. The above recommendation is merely for proteins.

> Argyris Karatrantos
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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