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On 9/12/2011 12:00 AM, Chandan Choudhury wrote:
<blockquote
cite="mid:CAHESojy+uFAvcT-4p+i3zimiEzOgHQ9Ym5k2GKa0X5iCc5Ja-Q@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">On Thu, Dec 8, 2011 at 12:33 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
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<div bgcolor="#FFFFFF" text="#000000">
<div class="im"> On 8/12/2011 2:54 PM, Chandan Choudhury
wrote:
<blockquote type="cite">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?</blockquote>
<br>
</div>
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 <a
moz-do-not-send="true"
href="http://redmine.gromacs.org/issues/834"
target="_blank">http://redmine.gromacs.org/issues/834</a>).<span
class="HOEnZb"><font color="#888888"><br>
<br>
Mark</font></span></div>
</blockquote>
<div><br>
</div>
<div>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.</div>
</div>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CAHESojy+uFAvcT-4p+i3zimiEzOgHQ9Ym5k2GKa0X5iCc5Ja-Q@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div> Actually, I dont have such a broad knowledge in C.</div>
</div>
</blockquote>
<br>
That's all the more reason to proceed by analogy from working code,
rather than try to write something from scratch.<br>
<br>
<blockquote
cite="mid:CAHESojy+uFAvcT-4p+i3zimiEzOgHQ9Ym5k2GKa0X5iCc5Ja-Q@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div> Can some one point me out what functions/variables should
be called in template.c (gmx_4.0.7) to obtain the box
vectors.</div>
</div>
</blockquote>
<br>
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...<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAHESojy+uFAvcT-4p+i3zimiEzOgHQ9Ym5k2GKa0X5iCc5Ja-Q@mail.gmail.com"
type="cite">
<div class="gmail_quote">
<div><br>
</div>
<div>Chandan</div>
<blockquote class="gmail_quote" style="margin:0 0 0
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<div class="im"><br>
<br>
<blockquote type="cite">
<div> <br>
</div>
<div>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. </div>
<div><br>
</div>
<div>Chandan<br clear="all">
<br>
--<br>
Chandan kumar Choudhury<br>
NCL, Pune<br>
INDIA<br>
<br>
<br>
<div class="gmail_quote">On Thu, Dec 8, 2011 at 3:33
AM, Mark Abraham <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au"
target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>On 8/12/2011 4:36 AM, Chandan Choudhury
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex"> <br>
Dear gmx_users,<br>
<br>
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?<br>
</blockquote>
<br>
</div>
g_energy on the .edr file (assuming that the
vectors actually vary).<span><font color="#888888"><br>
<br>
Mark</font></span>
<div>
<div><br>
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