[gmx-users] genbox -shell

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 15 18:54:16 CET 2005

Dongsheng Zhang wrote:
> Dear All,
> I made a extended peptoid molecule with 40 residues. When I solvate this
> molecule by genbox, I think it is a good idea to use -shell in order to
> avoid too many water molecules. 
> genbox -cp after_em_vac.gro -cs -p AcePoo40Nme_vac.top -c b4em -shell
> 1.0
> However, I find a few waters are far way from the peptoid molecule when
> I check the solvated system. Could anyone help me understand why this
> happens? Thanks in advance. The attached is part of the .gro file for
> the solvated system (I have modified it in order for someone to
> visualize it).
probably the input box is too small in the protein file

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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