<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><div>5 jun 2012 kl. 16.52 skrev Thomas Piggot:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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Hi,<br>
<br>
I think Erik meant to say that the program is trjorder (not g_order)
for the ordering of molecules by distance.<br>
<br>
Cheers<br>
<br>
Tom<br></div></blockquote><div><br></div>Indeed I did. Sorry, and thanks for the correction.</div><div><br></div><div>Erik</div><div><br><blockquote type="cite"><div text="#000000" bgcolor="#FFFFFF">
<br>
On 05/06/12 14:41, Erik Marklund wrote:
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<div>5 jun 2012 kl. 15.05 skrev Justin A. Lemkul:</div>
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<br>
On 6/5/12 9:02 AM, rankinb wrote:<br>
<blockquote type="cite">I am interested in pulling out the
trajectories (x,y,z coordinates) of water<br>
</blockquote>
<blockquote type="cite">molecules within a certain distance
of my solute molecule. I have tried<br>
</blockquote>
<blockquote type="cite">using g_select, but that will only
give me the atom numbers and not the<br>
</blockquote>
<blockquote type="cite">trajectories. I can create an index
file using this command but<br>
</blockquote>
<blockquote type="cite">unfortunately each time frame is set
as a different group.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Is there a way to get the
trajectories at all frames of only the water<br>
</blockquote>
<blockquote type="cite">molecules within a specified
distance of a solute molecule?<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<br>
At present, there is no elegant way to construct such a
trajectory, since, in principle, each frame can have a
different number of atoms based on which water molecules
satisfy the given criteria. Each index group that g_select
provides corresponds to an individual frame in the original
trajectory, which you can use to pull out individual
coordinate files. Perhaps a multi-frame .pdb or .gro file
would work, but I believe that .xtc and .trr files have to
have the same number of atoms in each frame to be
interpreted correctly.<br>
<br>
-Justin<br>
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</blockquote>
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<div>g_order orders the molecules according to distance to
solute. Then you can pick out the N first from each frame. It
is, however, a bit cumbersome for an entire trajectory.</div>
<div><br>
</div>
<div>Erik</div>
<br>
<blockquote type="cite">
<div><br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul, Ph.D.<br>
Research Scientist<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]vt.edu | (540) 231-9080<br>
<a moz-do-not-send="true" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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<div>-----------------------------------------------</div>
<div>Erik Marklund, PhD</div>
<div>Dept. of Cell and Molecular Biology, Uppsala
University.</div>
<div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div>
<div>phone: +46 18 471 6688 fax: +46 18 511
755</div>
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<pre class="moz-signature" cols="72">--
Dr Thomas Piggot
University of Southampton, UK.
</pre>
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<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>-----------------------------------------------</div><div>Erik Marklund, PhD</div><div>Dept. of Cell and Molecular Biology, Uppsala University.</div><div>Husargatan 3, Box 596, 75124 Uppsala, Sweden</div><div>phone: +46 18 471 6688 fax: +46 18 511 755</div><div><a href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a></div><div><a href="http://www2.icm.uu.se/molbio/elflab/index.html">http://www2.icm.uu.se/molbio/elflab/index.html</a></div></div></span></div></span></span>
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