[gmx-users] Re:genbox -shell

David spoel at xray.bmc.uu.se
Tue Nov 22 17:36:13 CET 2005

On Tue, 2005-11-22 at 23:50 +0800, Wang Zhun wrote:
> Hi, David,
> I used -shell and PBC at the same time, but through ngmx I found the peptide chain in water had some amino acid residues exposed out of water which formed a sphere  after about 1 ns during MD simulation.
> Should I increase the thickness of the water shell?
You probably can not avoid this completely without using full PBC.

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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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