[gmx-users] box vectors - regd
rameshgromacs at gmail.com
Thu Aug 16 07:22:38 CEST 2012
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
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, if so how can i extract
Please suggest me a way.
On Thu, Aug 16, 2012 at 4:52 AM, Mark Abraham <Mark.Abraham at 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
> 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.
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