[gmx-users] box vectors entry in "gro" file

[Makoto Yoneya]

Dear David/Tsjerk:

> Could someone kindly teach me the exact translate formulas 
> from PDB file CRYST1
> entry of "a, b, c, alpha, beta, gamma"
> to the gro file entry "XX YY ZZ XY XZ YX YZ ZX ZY" above?

I found the formula above as follows.

xx = a
xy = 0.0
xz = 0.0
yx = b*cosgam
yy = b*singam
yz = 0.0
zx = c*cosbet
zy = (c/singam)*(cosalp-cosbet*cosgam)
zz = v/(a*b*singam)
here,
v = sqrt(1.0 - cosalp**2 - cosbet**2 - cosgam**2 +
2.0*cosalp*cosbet*cosgam)*a*b*c

Results of this formula agree with the translation with editconf.
Thanks a lot for your comments.

Makoto Yoneya, Dr.
AIST, Japan