[gmx-users] box vectors - regd
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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