[gmx-users] genbox -shell

[David van der Spoel]

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.
________________________________________________________________________
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++