[gmx-users] (no subject)

David van der Spoel spoel at xray.bmc.uu.se
Sun Oct 5 14:33:10 CEST 2008

Sunil Thapa wrote:
> hello gmx users
> I am a new fellow in gromacs
> My structure contains 56 residues belonging to parallel helices 
> separated by about 2 nm.
> I used editconf as:
> editconf----- -bt dodecahedron -c
> and
> editconf---- -bt dodecahedron -d 6.5 -c
> where 6.5nm I used as separation of unit cells
> Now when I solvated using spc216. In the first case, the number of 
> solvent molecules was more than 117000 and in the second case it was 
> 704. Moreover, in both the cases large number of atoms lied outside the box.
> Can you tell me how to know the appropriate size of box for a protein 
> structure like mine
how about 1 nm (10 angstrom)?
> Thanks in advance
> Neal 
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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