[gmx-users] genbox problem with micelle

David van der Spoel spoel at xray.bmc.uu.se
Mon Jun 4 09:58:16 CEST 2007

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 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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