[gmx-users] Simulated annealing (now genbox)

[David van der Spoel]

On Thu, 2003-07-31 at 23:28, Albert Sun wrote:
> How can we use other molecules to replace protein and solvent when
> using genbox?
> could we use other .gro files to replace protein.gro and spc216.gro ? 
yes, the only restriction is that the solvent should be one residue per
molecule. e.g. dmso.gro could be used. You can also use mixed solvent,
i.e. you can start with an equilibrated water/methanol box and solvate
your protein in that.
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> Osmany Guirola Cruz <osmany.guirola at cigb.edu.cu> wrote:
>         Thanks Xaviier
>         
>         
>         Xavier Periole wrote:
>         >  
>         >         
>         >         1) How can i use genbox to insert extramolecules of
>         >         solvent?
>         >         
>         >         
>         >          
>         > a simple genbox -h gives you the answer. But basically
>         > something like :
>         >  
>         > genbox -cp protein.gro -cs spc216.gro -nmol <number of
>         > molecules you want> 
>         >             -try ......
>         >  
>         > take a look.
>         >  
>         > XAvier
>         >  
>         >  
>         
> 
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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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