[gmx-users] Re: genbox -shell

[David van der Spoel]

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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++