[gmx-users] Optimizing system size by moving from rectangular to hexagonal cells
chunleizhang.pku at gmail.com
Fri Jun 25 10:05:35 CEST 2010
I think you may try "trjconv -ur".
2010/6/25 Marc Baaden <baaden at smplinux.de>
> Dear All,
> Trying to optimize some simulation systems, I noticed that I could
> actually gain quite some degrees of freedom by changing the xy
> dimension of my simulation system from square/rectangular to hexagonal.
> I wonder how one would do that in order to preserve at best the
> properties of an already equilibrated system with a rectangular
> xy-plane. Can Gromacs simply "cut" a hexagonal patch out of a periodic
> simulation box with rectangular geometry?
> Which tool would one use for this task? Editconf, with options eg
> -c -box a b c -angles 120 120 90 ?
> Thank you very much in advance,
> Marc Baaden
> Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
> mailto:baaden at smplinux.de - http://www.baaden.ibpc.fr
> FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
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