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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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