[gmx-users] box vectors

[Chandan Choudhury]

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.
Actually, I dont have such a broad knowledge in C. Can some one point me
out what functions/variables should be called in template.c  (gmx_4.0.7)
 to obtain the box vectors.

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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