AMBER Archive (2006)

Subject: AMBER: Truncated octahedral box as triclinic lattice vectors

From: Markus O Kaukonen (mokaukon_at_cc.helsinki.fi)
Date: Mon Feb 20 2006 - 08:42:45 CST

Dear All,

In order to import AMBER files to NAMD one needs information of the
simulation box.

Could some one confirm that the simulation box of
truncated octahedron generated by leap command
solvateoct

gives a triclinic box with lattice vectors

a= [d 0 0]
b= [-d/3 2/3*sqrt(2)*d 0]
c= [-d/3 -1/3*sqrt(2)*d -1/3*sqrt(6)*d ]

where d == Box X = Box Y = Box Z given in amber output.

Terveisin, Markus 

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