Re: Why RDF increases as r increase instead of constant

From: Arash Azari (
Date: Mon Nov 03 2014 - 01:32:27 CST

Besideswhat Axel mentioned in VMD list, RDF is kind of measure for wellequilibrated system which means you should run your simulation forenough long time. Depending on the size of your system, probably youneed at least a few hundred picoseconds. Therefore, you should usethe frames towards the end of your simulation and leave the beginningframes. It seems up to now, your simulation has 20000 frames which isvery short simulation.Hopethis helps.

Bestregards,Arash  Arash Azari

     On Sunday, November 2, 2014 12:09 AM, 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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