[gmx-users] box vectors

[Tsjerk Wassenaar]

Hey,

On a general note, assuming the frame is read in as a t_trxframe
structure called frame, the box is accessible as frame.box and is a
matrix instance, which means it's a 3x3 array, containing the
triclinic box as a lower triangular matrix. If the code says
t_trxframe *frame somewhere, rather than t_trxframe frame, then you
need to access the box as frame->box in stead of frame.box. You can
find both in different gromacs tools.

Cheers,

Tsjerk

On Thu, Dec 8, 2011 at 2:46 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 9/12/2011 12:00 AM, Chandan Choudhury wrote:
>
>
> On Thu, Dec 8, 2011 at 12:33 PM, Mark Abraham <Mark.Abraham at anu.edu.au>
> wrote:
>>
>> On 8/12/2011 2:54 PM, Chandan Choudhury wrote:
>>
>> Thanks everyone for the responses. I should have framed my question much
>> more precisely. I am trying to use the template.c code of (gmx_4.0.7) and
>> within this, I want to take care of PBC. To do this, I should be having the
>> knowledge of box dimensions. How can this done?
>>
>>
>> Check out the code of g_bond or g_dist to see how to get access to the box
>> information from the trajectory, and how that might be used. Note that it's
>> important to get the data from the trajectory frame rather than the .tpr
>> when the former varies, and I am not sure that the code of those tools does
>> this correctly at the moment, or in 4.0.7 (see
>> http://redmine.gromacs.org/issues/834).
>>
>> Mark
>
>
> Thanks Mark for the response.  I did look at the code of g_hbond and
> g_dist. Truly speaking, I couldnot decode any information from it.
>
>
> Search the text for the variables "box" and "pbc" and see how they
> interact... Key here is to recognize that MD trajectories are normally too
> large to slurp into memory and then do operations on, so the code has to be
> structured to work on the trajectory frame by frame.
>
>
> Actually, I dont have such a broad knowledge in C.
>
>
> That's all the more reason to proceed by analogy from working code, rather
> than try to write something from scratch.
>
>
> Can some one point me out what functions/variables should be called in
> template.c  (gmx_4.0.7)  to obtain the box vectors.
>
>
> That's as hard as writing the code oneself... we don't even know that the
> reason you want to get these vectors at C level is worth writing C code
> for...
>
> Mark
>
>
>
> Chandan
>>
>>
>>
>>
>> I also know that the g_energy prints the box vector with the simulation
>> time. But, trjconv -dump also writes the box vectors in the pdb file.
>>
>> Chandan
>>
>> --
>> Chandan kumar Choudhury
>> NCL, Pune
>> INDIA
>>
>>
>> On Thu, Dec 8, 2011 at 3:33 AM, Mark Abraham <Mark.Abraham at anu.edu.au>
>> wrote:
>>>
>>> On 8/12/2011 4:36 AM, Chandan Choudhury wrote:
>>>>
>>>>
>>>> Dear gmx_users,
>>>>
>>>> I am using gmx_4.0.7. I need to print the box vectors from the
>>>> trajectory of a simulated system. How can this be achieved? Can someone help
>>>> me out?
>>>
>>>
>>> g_energy on the .edr file (assuming that the vectors actually vary).
>>>
>>> Mark
>>>
>>> --
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>>
>>
>>
>>
>>
>>
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>
>
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands