[gmx-users] Re:genbox -shell
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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