VMD-L Mailing List

From: Nifeng Guo hui (nifenggaohui_at_gmail.com)
Date: Sun Nov 02 2014 - 16:01:29 CST

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


RDF.png