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On 28/02/2012 10:49 AM, Sanku M wrote:
<blockquote
cite="mid:1330386556.59745.YahooMailNeo@web114402.mail.gq1.yahoo.com"
type="cite">
<div style="color:#000; background-color:#fff; font-family:times
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<div>Hi,</div>
<div> I have run a simulation of a fixed object in water using
gromacs. Now, I want to analyze only water molecules which are
present within a cylinder of certain radius (smaller than
simulation box dimension in XY plane).</div>
<div>I wonder whether gromacs has any particular tool which can
identify the particles within a cylindrical volume of a
simulation box.</div>
<br>
</div>
</blockquote>
<br>
g_select can make such a selection from a trajectory frame and write
it to an index file, but the diffusion of the water over time will
be a problem for a static selection. The kind of dynamic selection
you would want is not yet available. You could make do by scripting
g_select and some subsequent analysis tool inside a shell loop.<br>
<br>
Mark<br>
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