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On 4/05/2012 4:03 AM, mu xiaojia wrote:
<blockquote
cite="mid:CABSFTFp9CEQg_OuhQrgdPZ+MZ8jAyd9Hh+23YK5-pHNqnAUqrw@mail.gmail.com"
type="cite">Thanks Justin and Mark,
<div><br>
</div>
<div>I compared g_rama's results for no pbc treated trajectory and
pbc treated trajectory, it seems they are the same. So gromacs'
analysis tools know how to deal with the "broken" molecules. <br>
</div>
</blockquote>
<br>
Caveat: some tools seem to be better than others at dealing with
PBC. There are known question marks hovering over g_dist, g_bond and
g_mindist. This situation is probably a consequence of different
tools being developed at different times during the evolution of the
software suite.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CABSFTFp9CEQg_OuhQrgdPZ+MZ8jAyd9Hh+23YK5-pHNqnAUqrw@mail.gmail.com"
type="cite">
<div><br>
</div>
<div>But if one want to extract such coordinates out for computing
it myself, it is necessary to -pbc mol first, otherwise the
molecules might be "broken" for calculating scripts like matlab.</div>
<div><br>
</div>
<div>good to know this, thanks!</div>
<div><br>
</div>
<div><br>
<br>
<div class="gmail_quote">On Wed, May 2, 2012 at 8:03 PM, 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>
<div> </div>
<div> </div>
<span>On 03/05/12, <b>mu xiaojia </b><<a
moz-do-not-send="true"
href="mailto:muxiaojia2010@gmail.com" target="_blank">muxiaojia2010@gmail.com</a>>
wrote:</span>
<blockquote style="BORDER-LEFT:#00f 1px
solid;PADDING-LEFT:13px;MARGIN-LEFT:0px" type="cite"><font
size="4">Dear gmx users,</font>
<div><font size="4"><br>
</font></div>
<div><font size="4">I have a question about using the
trjconv -pbc options before analyzing my trajectory.
It's stated by Justin's tutorial that:</font></div>
<div><font size="4"><br>
</font></div>
<div><span style="FONT-FAMILY:Arial">
<p><font size="4">"use trjconv to account for any
periodicity in the system. The protein will
diffuse through the unit cell, and may appear to
"jump" across to the other side of the box. To
account for such actions, issue the following:</font></p>
<pre><font size="4">trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact"</font></pre>
<pre><font size="4">(<a moz-do-not-send="true" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/09_analysis.html</a></font></pre>
<pre><font size="4">)</font></pre>
<pre><font size="4">
</font></pre>
<pre><font size="4">But for my system, I study the short peptides' aggregation, I have many short peptides(not one or two single proteins) and waters, when I use -pbc nojump to treat my trajectory, it only gives me correct short peptides(no across out of the box), but the water is quite diffused. (I guess it is different with the tutorial since on it the protein is 1 or 2 polymers)</font></pre>
<pre><font size="4">
</font></pre>
<pre><font size="4">So (1)how should I analyze such results if I want to study both short peptides(correct coordinates, no crossings) and waters(diffused and crossed box)?</font></pre>
</span></div>
</blockquote>
<div> </div>
</div>
<div>That entirely depends on what you are trying to
observe. You may find you need multiple representations of
the trajectory for different purposes.</div>
<div>
<div> </div>
<blockquote style="BORDER-LEFT:#00f 1px
solid;PADDING-LEFT:13px;MARGIN-LEFT:0px" type="cite">
<div>
<div><span style="FONT-FAMILY:Arial">
<pre><font size="4">(2) I tried all the pbc options(even try them one after another, like mol first, nojump second), currently no clues of how to get both peptides and waters correct at the same time.　Command for correct protein but incorrect waters' coordinates is:</font></pre>
<pre><font size="4"><span style="FONT-FAMILY:Arial;WHITE-SPACE:normal;FONT-SIZE:small"><pre><font size="4">trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc nojump</font></pre>
<pre><font size="4">
</font></pre><pre><font size="4">Thanks very much, I appreciate any suggestions.</font></pre></span></font></pre>
</span></div>
</div>
</blockquote>
<div> </div>
</div>
<div>If molecules diffuse across the periodic boundaries,
you cannot have a single representation that is both
compact and lacks jumps.</div>
<span><font color="#888888">
<div> </div>
<div>Mark</div>
</font></span><br>
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