[gmx-users] simulation box

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Feb 12 16:19:04 CET 2006

Hi Phuong,

There is no box in your simulation system; All coordinates are Cartesian
coordinates. Read the manual better with regards to periodic boundary
conditions or check JCC 18:1930 (1997) (or alternatively JCC 25:1037 (2004))
by Henk Bekker. You could also search the archive for previous posts
concerning periodic boundary conditions.



On 2/11/06, Nguyen Hoang Phuong <phuong at theochem.uni-frankfurt.de> wrote:
> 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.
> Phuong
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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