From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Sun Nov 02 2014 - 12:38:04 CST
- 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: http://en.wikipedia.org/wiki/Radial_distribution_function
.. 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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