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On 4/29/2011 11:29 AM, shivangi nangia wrote:
<blockquote
cite="mid:BANLkTimFTDt74RV1HDoSvC3_hwQ_6gTuug@mail.gmail.com"
type="cite">Hello,<br>
<br>
The manual explaining trjorder says:<br>
<br>
trjorder orders molecules according to the smallest distance
to atoms in a reference group
or on z-coordinate (with option <tt>-z</tt>).
With distance ordering, it will ask for a group of reference
atoms and a group of molecules. For each frame of the trajectory
the selected molecules will be reordered according to the shortest
distance between atom number <tt>-da</tt> in the molecule and all
the
atoms in the reference group. <b>The center of mass of the
molecules can
be used instead of a reference atom by setting <tt>-da</tt> to
0</b><br>
<br>
In order to arrange water molecules in accordance with the COM of
the polypeptide, I chose -da 0.<br>
</blockquote>
<br>
As it says above, -da refers to an atom or COM of the molecule, not
the reference group. This could be worded better in the
documentation.<br>
<br>
Be sure you're choosing the groups you think you are choosing - you
not copying relevant parts of your terminal output into emails is
making things difficult.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTimFTDt74RV1HDoSvC3_hwQ_6gTuug@mail.gmail.com"
type="cite"><br>
Am I wrong?<br>
<br>
Thanks,<br>
SN <br>
<br>
<br>
<br>
<br>
<div class="gmail_quote">On Thu, Apr 28, 2011 at 8:29 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>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
On 4/29/2011 4:08 AM, shivangi nangia wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Hello all,<br>
<br>
I am trying to order the TIP4P water molecules in my system
with respect to the polypeptide in my system.<br>
<br>
The command I am using is:<br>
<br>
trjorder -f shape.gro -s shape.tpr -da 0 -na 4 -o
ordered.gro<br>
<br>
This runs without any error and ordered.gro is generated
with random sequence of water molecules.<br>
<br>
Just to cross check I calculated the distances between one
of atoms of the polypeptide and oxyegn atom of different
"ordered" water molecules.<br>
I found, there is no ascendig trend in the distances with
respect to the polypeptide as a go down in the "ordered.gro"
file.<br>
<br>
What could be going wrong?<br>
</blockquote>
<br>
-da 0 has a particular effect - is it appropriate? Did you
choose the right groups? You could use the -nshell option to
probe what trjorder thinks is going on.<br>
<br>
Mark<br>
<font color="#888888">
<br>
<br>
<br>
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</blockquote>
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