On 16/08/2012 3:22 PM, ramesh cheerla wrote:
Dear Mark,
Thank you for your reply, as you suggested I will go
through the sec 7.4 and 8 of the manual and moreover how would I get
exact box vectors XX YY ZZ XY XZ YX YZ ZX ZY for each frame of
trajectory in gromacs
They're in the trajectory file with each frame.
As I am new to gromacs I have no Idea where these will be stored (
other than gro file ). In NAMD .XTC file contains box vectors for
each step of the simulation like this is there any file in gromacs
that stores these box vectors for each step,
Same.
if so how can i extract
them.
Probably however you did so with NAMD, or with g_traj or gmxdump.
Mark
Please suggest me a way.
Thank you.
On Thu, Aug 16, 2012 at 4:52 AM, Mark Abraham <mark.abra...@anu.edu.au> wrote:
On 16/08/2012 5:46 AM, ramesh cheerla wrote:
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
calculations.
Sounds like g_energy is reminding you that you had a rectilinear simulation
cell when you started, and still do. There are various ways to measure
angles that will help you address your problem, if you check out manual
sections 7.4 and 8.
Mark
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