[gmx-users] Re. genbox -shell

[Dongsheng Zhang]

Dear David,

I am confused by your reply. In your tutorial, you use
editconf .. -c -d 0.5

Now I am using -d 1.0, and 1.0 nm = 10 A, I don't understand why you
think the box is too small.

Thank you for your help!




> Message: 6
> Date: Thu, 15 Dec 2005 20:43:59 +0100
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] Re: genbox -shell
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <43A1C77F.8010001 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=UTF-8; format=flowed
> 
> Dongsheng Zhang wrote:
> > Dear David,
> > 
> > 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
> but a water is larger than 0 so you need e.g. editconf -d 2
> 
> > 
> > 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!
> > 
> > 
> > Best wishes!
> > 
> > 
> > 
> >>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.
> >>________________________________________________________________________
> >>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>