[gmx-users] rhombic dodecahedron membrane simulations

[David van der Spoel]

On Fri, 2003-08-22 at 11:42, Krzysztof Murzyn wrote:
> Hi all,
> 
> I'd like to perform an MD simulation of a lipid bilayer system using 
> rhombic dodecahedron periodic boundary conditions. My starting 
> configuration is in a rectangular box with dimensions, say, a, b and c 
> (a != b != c). I guess I should use editconf with -box A B C -angles 60 
> 60 60; however, to preserve box volume new box dimensions must be 
> somewhat bigger (by factor 1/sin(60) or so?).
> 
> Could someone give me any tips how to convert a rectangular box into a 
> rhombic dodecahedron box?
> 
How about:
editconf -f spc216.gro -bt dodecahedron -o ccc.gro -box 2.1 2.1 2.1

Check that the volume remains the same (or indeed sligthly larger) and
that your lipids don't break...
 

> Regards,
> Krzysztof
> 
> 
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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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