[gmx-users] box vectors

[Mark Abraham]

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 
> <mailto: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 <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
>>
>>         -- 
>>         gmx-users mailing list gmx-users at gromacs.org
>>         <mailto:gmx-users at gromacs.org>
>>         http://lists.gromacs.org/mailman/listinfo/gmx-users
>>         Please search the archive at
>>         http://www.gromacs.org/Support/Mailing_Lists/Search before
>>         posting!
>>         Please don't post (un)subscribe requests to the list. Use the
>>         www interface or send it to gmx-users-request at gromacs.org
>>         <mailto:gmx-users-request at gromacs.org>.
>>         Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>>
>
>
>     --
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the
>     www interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111209/1cbb101a/attachment.html>