[gmx-users] box vectors - regd

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 16 07:47:35 CEST 2012

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,


>   if so how can i extract
> them.

Probably however you did so with NAMD, or with g_traj or gmxdump.


> Please suggest me a way.
> Thank you.
> 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
>>> 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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