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You can use g_order for that with just a bit of additional
scripting.<br>
<br>
Erik<br>
<br>
maria goranovic skrev 2011-05-10 09.17:
<blockquote
cite="mid:BANLkTinetnkVtR5WAAmQ4b40WY_j=Pfvpg@mail.gmail.com"
type="cite">So, one can probably do this using a simple script?
<div><br>
</div>
<div>for each frame</div>
<div><br>
</div>
<div>make index file of water molecules within 0.5 nm using
g_select</div>
<div>extract frame based on above selection</div>
<div><br>
</div>
<div>done</div>
<div>concatenate frames</div>
<div><br>
</div>
<div>The only problem with the above would be that the number of
water molecules selected might change with each frame. Is there
a way of choosing the closest, say, 1000 water molecules using
g_select<br>
<br>
<div class="gmail_quote">On Tue, May 10, 2011 at 12:28 AM, 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;">
<div class="im">On 10/05/2011 12:50 AM, maria goranovic
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Dear experts<br>
<br>
I have a protein simulation in a water box. I now want
to write a trajectory containing only the protein, and
water molecules within 5 Angstroms of the protein, with
the water list being updated each time step. How can one
do this? Appreciate the help<br>
</blockquote>
<br>
</div>
g_select is useful for "dynamic" selections of this type.
g_select -select "help" can give examples and such.<br>
<br>
I'd hope it's been designed so that then using trjconv to
extract such selections works, but I can't think how, having
not ever tried.<br>
<br>
Mark<br>
<font color="#888888">
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</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
Maria G.<br>
Technical University of Denmark<br>
Copenhagen<br>
</div>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
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