[gmx-users] rhombic dodecahedron membrane simulations
David van der Spoel
spoel at xray.bmc.uu.se
Fri Aug 22 13:55:01 CEST 2003
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?
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...
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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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