[gmx-users] NVT

[David van der Spoel]

Junfang.Zhang at csiro.au wrote:
> Dear Gromacs-users,
> 
>  
> 
> I am going to use Gromacs to simulate gas hydrates.
> 
> As I am new to this software, I am wondering if you can help me with 
> some questions.
> 
>  
> 
> Currently, I am looking at the system of water+methane. Can you please 
> let me know how to keep the total number of molecules fixed or specify 
> the number of water molecules and methane molecules?
> 
>  
> 
>  If I use the following command
> 
>  
> 
> Genbox  -cs  water.gro  -ci    methane.pdb –nmol 8 –box 2 2 2 –o out.gro
> 
>  
> 
> to generate out.gro file, the number of methane molecules  can be 
> specified, but not the water molecules.
correct. Make a slightly larger box and manually remove the surplus 
water from the gro file.

> 
>  
> 
>  
> 
> Your assistance will be deeply appreciated.
> 
>  
> 
> Regards and thanks,
> 
>  
> 
>  
> 
> Jane
> 
>  
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>  
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>  
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> 
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> 
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-- 
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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