[gmx-users] Re. genbox -shell

[David van der Spoel]

Dongsheng Zhang wrote:
> 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!
just try it.

> 
> 
> 
> 
> 
>>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
>>>>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>>>>
>>>>
>>>>------------------------------
>>>
>>>


-- 
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
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