<div class="gmail_quote"><br></div><div class="gmail_quote"><br></div><div class="gmail_quote">On Thu, Jan 19, 2012 at 12:17 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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div>On 19/01/2012 5:39 PM, 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 have a simulated a system containing a linear polymer in a cubic box with water molecules. I need to get rid of PBC effect on the system such that I can execute my own analysis code. I intend to compute the msd of water molecules along the polymer backbone.<br>
</blockquote>
<br></div>
You can't "get rid of PBC", you can only manage it. The question reduces what you want to see if a molecule diffuses across the periodic boundary from near one end of the polymer to the other end.<div>
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
So, when I execute my own analysis code, I see the msd's are abrupt (i.e very high), this is due to the pbc. So, for getting rid of PBC effect, I performed the suggested trjconv workflow (<a href="http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions" target="_blank">http://www.gromacs.org/<u></u>Documentation/Terminology/<u></u>Periodic_Boundary_Conditions</a>). <br>
<br>
Below are my executed commands :<br>
<br>
# Made the system whole<br>
<br>
echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc whole -o 0-4_whole.xtc<br>
<br>
# 0 is the whole system. md0-4.tpr is the initial tpr file containing whole (no broken) polymer inside the cubic box.<br>
# Extracted 1st frame from the initial trajectory<br>
<br>
echo 0 | trjconv_4.5.5 -s md0-4.tpr -f 0-4.xtc -pbc nojump -o 1st.pdb -dump 0<br>
<br>
# used the whole trajectory to remove jumps with reference to the 1st frame.<br>
echo 0 | trjconv_4.5.5 -s 1st.pdb -f 0-4_whole.xtc -pbc nojump -o 0-4_nojump.xtc<br>
</blockquote>
<br></div>
So here you said "let molecules diffuse away from the solute".<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
#system is being centered<br>
echo "0 0" | trjconv_4.5.5 -s md0-4.tpr -f 0-4_nojump.xtc -o 0-4_center.xtc -center<br>
<br>
#putting every atom in the box<br>
echo 0 | trjconv -s md0-4.tpr -f 0-4_center.xtc -o 0-4_box.xtc -pbc atom<br>
</blockquote>
<br></div>
... and now you said "take all the atoms and put them back in the box", creating jumps whenever one crosses the boundaries.<div><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Still when I execute my analysis code, I do see the abrupt behaviour in the msd plot. Can someone guide me how to completely get rid of PBC artifacts.<br>
</blockquote>
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Don't simulate with them :-P Is your analysis technique sound for the periodic case?</blockquote><div><br></div><div>No, my analysis code doesnot take care of PBC. As to deal with PBC, I need to have the box vectors (for atleast NPT simulation) from the trajectory and I am unable to extract the box vectors (as of date).</div>
<div><br></div><div>Chandan</div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span><font color="#888888"><br>
<br>
Mark</font></span><div><div><br>
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<br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br><div>INDIA </div></div><br>