Re: Why RDF increases as r increase instead of constant

From: Kenno Vanommeslaeghe (
Date: Sun Nov 02 2014 - 18:25:41 CST

- Please reply to the list rather than personal e-mail (hint to the list
admin: Majordomo has an option to override the Reply-To: address!)

- The plot you attached does not even look quadratic; on second thought,
you might have plotted the integral of the normalized RDF, which would be
expected to be linear at long distances.

- If the hints I gave you so far are not sufficient to figure out the
problem, then ask again on the VMD list. Even if I knew exactly what
you're doing wrong (which I don't on account of never having used that VMD
plugin), I would be depriving you of a learning opportunity by giving you
a straight answer.

On 11/02/2014 04:15 PM, Nifeng Guo hui wrote:
> Thanks for your response. I did understand what an RDF is before I asked
> for help. It just because my plot is different with the predication one.
> Then here is the my question. From the definition of RDF, it implies the
> density change relative to a certain point. Thus, after certain distance
> from the reference point,the particles will distribute evenly since it is
> a homogeneous and isotr(rather than the unnormalized one, as I first assumed)ke topic system. However, in my plot, RDF owns
> an increasing trend as r increases. As you said, RDF features with
> quadratic function, it still confuses me why it's not horizontal. I
> attached the plot along with this email. Please take a look at it. Thanks.
> Peng
> 2014-11-02 12:38 GMT-06:00 Kenno Vanommeslaeghe <
> <>>:
> - Wrong list - try the VMD list in the future.
> - Question can be answered by looking up what an RDF is and how it is
> calculated:
> <>
> .. which is something you should always do before asking questions.
> - Not every function with a strictly positive second derivative is
> exponential. Yours is quadratic. The difference is important.
> On 11/01/2014 06:07 PM, Nifeng Guo hui wrote:
> Dear NAMD users,
> We perform one simulation with one protein immersed in water. Now,
> we want
> to analyze the water distribution around this molecule after finishing
> production run. The g(r) GUI Plugin, Version 1.3 was applied to
> calculate
> its function. After I input PSF and DCD files, I put "residue 1 to
> 36" in
> Section 1 and "water" in Section 2. (This protein is composed of
> 36 amino
> acids. ) I also tried "protein" for Selection 1. Next, Frames are
> "0" in
> First and "19999" in Last. Then before using compute g(r), I
> select Use
> PBC, Display g(r), and Display int(g(r)). However, the result does not
> reach our predictions. The RDF and Coordination number are both
> increasing
> exponentially as r increase. In our prediction, it supposes to become
> constant. Could you help me find what cause this? Thanks.
> Peng

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