From: Nifeng Guo hui (nifenggaohui_at_gmail.com)
Date: Sat Nov 01 2014 - 17:07:32 CDT
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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