Hello,<br><br>Came back to the set of calculations I was doing few days back.<br><br>I have a box of water (TIP4P), methanol, protein and DHB anions.<br><br>I minimized this system.<br><br>Trying to use trjorder for water molecules with respect to the protein (eventually I want to make a sphere by ordering and getting rid of the molecules I do not want)<br>
<br>In the index.ndx file i specified atom "144" (belongs to protein)<br><br>so when I run<br><br> trjorder -f em.gro -s em.tpr -n index.ndx -na 4 -o ordered.gro<br><br>I pick number associated with atom "144" and SOL ( tip4p water) and I generate ordered.gro<br>
<br>The sequence for SOL changes ( random), but when I use g_dist as I go down the ordered.gro, there is still no trend ( ascending with respect to protein)<br><br><br><br><br><br>Also, -da 0 refers to an atom OR COM of the molecule.<br>
using trjorder -f em.gro -s em.tpr -n index.ndx -da 0 -na 4 -o ordered.gro and running it <br><br>and choosing "1" for protein and "14" for SOL means that gromacs automatically understands that protein's COM is to be used to order SOL (tip4p, -na 4) ?? <br>
<br>If so, then tha talso generates a .gro file which produces random water molecules but there is again no trend.<br><br>I am very confused about using trjorder, it will be really helpful if someone or Mark can help me understand.<br>
<br>Thanks a lot<br>SN<br><br><br><div class="gmail_quote">On Thu, Apr 28, 2011 at 9:43 PM, Mark Abraham <span dir="ltr"><<a 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;">
<div bgcolor="#ffffff" text="#000000">
On 4/29/2011 11:29 AM, shivangi nangia wrote:
<blockquote 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 type="cite"><br>
Am I wrong?<br>
<br>
Thanks,<br>
SN <br><div><div></div><div class="h5">
<br>
<br>
<br>
<br>
<div class="gmail_quote">On Thu, Apr 28, 2011 at 8:29 PM, Mark
Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">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>
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