[gmx-users] Optimizing system size by moving from rectangular to hexagonal cells

Marc Baaden baaden at smplinux.de
Fri Jun 25 09:13:26 CEST 2010

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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