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Thanks Justin,<br>
The edr file is binary and I don't know how to access it.<br>
I had seen that the gro file contains the vectors, and the
documentation says the following:<br>
<i><br>
box vectors (free format, space separated reals), values: v1(x)
v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)</i><br>
<br>
However I still don't know what these components are and how to
relate that to a dodecahedron, truncated octahedron, etc.<br>
In particular, my file contains:<br>
<br>
13.27362 13.27362 9.38587 0.00000 0.00000 0.00000
0.00000 6.63682 6.63682<br>
<br>
Thanks again,<br>
Ramon<br>
<br>
<br>
<blockquote type="cite">
<pre>On 11/3/15 5:56 AM, Ramon Crehuet wrote:
><i> Dear all,
</i>><i> This is a very simple question, but I could not find the answer in the
</i>><i> documentation. Some time ago I run a simulation and now I don't remember the box
</i>><i> shape and sizes I used. In which file is this information contained?
</i>><i> A related question is whether the box volume is printed somewhere or I need to
</i>><i> calculate it from the parameters.
</i>><i> Thanks in advance,
</i>><i> Ramon
</i>><i>
</i>><i> PS. My log contains Box-X Box-Y and Box-Z parameters. Does that mean I used a
</i>><i> rectangular box?
</i>><i>
</i>
Box vectors are stored in the .edr file, and you can verify the shape from the
vectors printed to any coordinate file (your starting coordinates, dumped from
the .tpr if needed, or any final coordinate file printed by mdrun).
-Justin</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="80">--
Ramon Crehuet
Cientific Titular (Assistant Professor)
Institute of Advanced Chemistry of Catalonia
IQAC - CSIC
<a class="moz-txt-link-freetext" href="http://www.iqac.csic.es/qteor">http://www.iqac.csic.es/qteor</a>
<a class="moz-txt-link-freetext" href="https://twitter.com/rcrehuet">https://twitter.com/rcrehuet</a>
<a class="moz-txt-link-freetext" href="http://ramoncrehuet.wordpress.com/">http://ramoncrehuet.wordpress.com/</a>
Tel. +34 934006116
Jordi Girona 18-26
08034 Barcelona (Spain) </pre>
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