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 href="mailto:Mark.Abraham@anu.edu.au">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 class="im">On 10/05/2011 12:50 AM, maria goranovic wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;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">
-- <br></font><div><div></div><div class="h5">
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