VMD-L Mailing List

From: Tim Lo (timlo_at_hku.hk)
Date: Sun Nov 02 2014 - 19:19:57 CST

Hi Peng,

By looking at the r-axis, the graph just displays g(r) for the range of
[0, 10]. You should increase "max r" to your desired value, but not just
use the default value of 10.0.

Tim

On 2014/11/3 上午 06:01, Nifeng Guo hui wrote:
> Dear VMD 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? Plese also take a look at the plot in
> the attachment. Thanks.
> Peng
>
>
>