[gmx-users] genbox problem with micelle

[David van der Spoel]

Alif M Latif wrote:
> Dear GROMACS users and developers..
>  
> I'm trying to run MD simulation on a micelle structure, which i've built 
> using Packmol. The problem is when i use genbox to solvate the system 
> using SPC water, the water came inside the micelle, and my simulation 
> didn't produce any significant changes to the structure (the behavior of 
> lipids which are lipophilic should squeezed the water molecules outside 
> the micelle structure). I'm wondering if i can tell genbox not to put 
> water molecule inside the micelle...can i?.. :-p
>  
> Thanks 4 reading...any comments and suggestion will be greatly appreciated..
>  
A third alternative would be to increase the vdw radii, by copying 
vdwradii.dat to your working directory and increase the water radius.

-- 
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://folding.bmc.uu.se
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