[gmx-users] box vectors - regd

ramesh cheerla rameshgromacs at gmail.com
Wed Aug 15 21:46:56 CEST 2012

Dear Gromacs users,

         I am using gromacs for simulations of a polymer,  for that  I
am planing to see how  lattice parameters a , b & c are varying
during simulation. Here lattice parameter "a" is the length of unit
cell  along X- direction, "b" is the length of the unit cell along
"Y" axis and "c"  is along Z -axis.
For my polymer polymer chains are not exactly oriented  along Z-
direction they are  a little bit tilted from the Z- axis.  "a" and "b"
are  along "x" and "Y"  directions respectively so that I can get
lattice parameters "a" and "b" just by dividing box lengths along
those directions with the number of  unit cells in those directions.
As the c- direction and Z- direction are not exactly same ( "c" is a
little bit tilted from Z ) in this case I shouldn't divide the box
length along Z - direction with the number of unit cells in that
direction to get lattice parameter "c". Here my questions are:
1) How can I calculate exact  "C" lattice parameter from simulation
data ? is there any way to get appropriate "c"?
2) How one can get box vectors XX YY ZZ XY XZ YX YZ ZX and  ZY  for
total trajectory, as g_energy is giving only Box - X , Box-Y  and Box-
Z but i need exact box vectors for valid lattice parameters

Any help will be highly appreciated.

Thank you in advance.


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