[gmx-users] Re: genbox -shell
dong at pampas.chem.purdue.edu
Thu Dec 15 20:40:56 CET 2005
Thank you for your reply. My input box is pretty large. The dimensions
are: 9.46000 6.52700 14.59200. They are generated by
editconf ... -c -d 1.0
the thickness of my shell is 1.0, I think it is large enough for those
water molecules. Most water molecules are inside the shell, only those
three are far way.
If you need more information, please let me know!
> Message: 1
> Date: Thu, 15 Dec 2005 18:54:16 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] genbox -shell
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <43A1ADC8.5090001 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 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
Dongsheng Zhang <dong at pampas.chem.purdue.edu>
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