[gmx-users] genbox -shell

David spoel at xray.bmc.uu.se
Sun Nov 20 10:40:13 CET 2005

On Sun, 2005-11-20 at 17:26 +0800, Wang Zhun wrote:
> Hi, gmxers,
> Usage of "genbox -shell" can add a layer of water around my peptide to decrease working load of MD simulation.
> I want to know how the thickness of the layer is decided,1nm or 2nm? A too thin layer may provide few water molecules while a too thick layer means unnecessary computation load. I'd like to know others' experience.

Remember that water will evaporate since there is no special potential
to keep it in the cluster,

PBC might be cheaper anyway.
> Thanks!
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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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