[gmx-users] simulation box

Nguyen Hoang Phuong phuong at theochem.uni-frankfurt.de
Sat Feb 11 19:05:23 CET 2006

Dear All,

I have performed simulations using truncated octahedral box. Three unit
vectors of the truncated octahedral box (t1, t2, t3) are related to their
counterpart (e1, e2, e3) in Cartesian coordinate system by the
relationship listed in page 13 of the gromacs's manual.

If I want to analyse the trajectory, e.g. calculating the scalar product
between two vectors, calculating the distance etc. then I have to convert
the atomic coordinates obtained directly from simulations to Cartesian
coordinate system first?

I am not sure about this since in page 12 of gromacs's
manual it was written that "even when simulation was performed in triclinic box, gromacs always put
the particles in a brick shaped volume. It means that the coordinates in
the output traj. (simulated with truncated octahedral box) are always in
Cartesian system? Gromacs automatically convert the (t1, t2, t3) system to
the Cartesian coordinate system (e1, e2, e3) when output trajectory?

Thanks for any explaination.


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