[gmx-users] box vectors

[Mark Abraham]

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

>
> 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 
> <mailto: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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