Re: [AMBER] rdf

From: Thomas Cheatham III <>
Date: Tue, 18 Jan 2011 12:06:57 -0700 (Mountain Standard Time)

> I am caulcating RDF for a system containing carbohydrate and water.
> During calculating Rdf three file is generated..
> rdf_carnal.xmgr, rdf_volume.xmgr, rdf_standard.xmgr
> Is this necessary to all three plot are similar??
> In my case they are differ by almost one unit.

Yes, all should be similar (i.e. same shape), however where the values
level off to depends on the method. The "carnal" output is for backward
compatibility and can be ignored.

The difference in the final value (which should go to unity) depends on
the density (normalization factor). With the "standard", a density input
by the user is utilized (defaults to 1.0). With the "volume" the average
volume is used to normalize.



     * output Allen & Tildesley style histogram, i.e.
     * histogram[bin]
     * ----------------------------------------------------------
     * (4/3)*pi*density*[(R+delR)**3 - R**3] * frames * molecules

Where "R" is the current distance, "delR" is the spacing between frames,
and "histogram[bin]" is the count over that interval.


     * output Allen & Tildesley style histogram, but
     * use system volume rather than density...
     * histogram[bin] * volume
     * --------------------------------------------------
     * (4/3)*pi*[(R+delR)**3 - R**3] * frames * molecules

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Received on Tue Jan 18 2011 - 11:30:04 PST
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