[gmx-users] g_mindist, truncated octahedron and amber trajectory

[cailliez]

Dear all,

I am very interested in using g_mindist tool from the GROMACS package to
analyse
the minimum distance between a solute and its image during a simulation.
As I understand, g_mindist can read AMBER trajectory files when renamed
with g87 extension.
But I do not understand how g_mindist is working with box information.
In AMBER trajectories, box information that is written at the end of
coordinates only contains
the length of the three vectors of the box (even when this is an
truncated octahedron). The type of box
is contained in the topology file.
This does not seem to be written in the same way in g87 files, so when I
use my AMBER trajectory,
I think the images are created assuming that my box is orthorombic.
I did not manage to solve this problem.
I tried to transform my AMBER trajectory replacing the box info by
another box info written as :
v1(x) v1(y) v1(z) v2(x) v2(y) v2(z) v3(x) v3(y) v3(z) or v1(x) v2(y)
v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y) (as in gro format).
But g_mindist seems to read only the three first numbers for the box and
says to me "Warning: Triclinic box is too skewed" (which
it does not say when I enter my initial AMBER trajectory).

I would appreciate any help,
Thank you in advance,
Fabien

-- 
__________________________________________________________________
Fabien Cailliez				Tel : 01 58 41 51 63				
Laboratoire de Biochimie Théorique	e-mail : cailliez at ibpc.fr
IBPC	13, rue Pierre et Marie Curie 		
75005 Paris					
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