AMBER Archive (2006)

Subject: AMBER: Truncated octahedral box as triclinic lattice vectors

From: Markus O Kaukonen (
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

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

-----------www=  \ HOME->   Viinirinne 3 F 12
Dep. of Theoretical Chemistry  \_______  02630 Espoo, Finland
Lund University                 \ tel:+358-(0)9-5127122/h
Chemical Centre, P. O. Box 124   \____
S-221 00, Lund, Sweden             \______ H+ ______
--- Rikos ei kannata, eika maatalous Suomessa. (Paimio 1998) ---
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to