[gmx-users] box vectors - regd

[ramesh cheerla]

Dear Mark,

            Once again I am very thankful to you for your reply, I
have  extracted box vectors from .XTC file  by using  g_traj with  -ob
 option with this I was able to get only six vector components viz  XX
YY ZZ  YX  ZX  and ZY only how about remaining three vector components
XY XZ and  YZ .
I have used triclinic box for my simulations I know that XY XZ and YZ
will be zero, moreover  I have used " pcoupltype      = anisotropic "
with compressibility values as "compressibility = 4.5e-5  4.5e-5
4.5e-5  0.0  0.0  0.0"  in my .mdp file.
Here my question is why I am not getting XY XZ and  YZ components in
my output file though they might be zero. Is this because of above
specified .mdp options  or something else ?
Can you please let me know what might be the probable reason ?

Thank you in advance.


On Thu, Aug 16, 2012 at 11:17 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> 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.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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