From: Dan Bolintineanu (dan.bolintineanu_at_gmail.com)
Date: Tue Jul 28 2009 - 16:50:37 CDT
I've been trying to do some FEP calculations using NAMD, and have been
experimenting with the ethane-ethane zero-sum calculation in the NAMD
FEP tutorial to get a feel for FEP calculations. I found the results
a bit surprising, and was hoping someone could shed some light on
Using NAMD 2.7b1 with
I obtain a satisfactory final result, about -0.002 kcal/mol. However,
the lambda vs. delta G plot looks nothing like the one in the
tutorial; it decreases linearly to about -7 kcal/mol, after which it
increases linearly to -0.002 kcal/mol.
In NAMD 2.6, using the exact same input file and sampling strategy,
but commenting out the three lines above, I obtain a final result of
+0.2 kcal/mol, but a delta G plot that seems much more reasonable,
very similar to the one in the tutorial (except for the endpoint).
In both cases, I have used much higher sampling (larger # of windows)
than indicated in the FEP tutorial. I've attached my input file for
the NAMD 2.7b1 run.
My questions are:
1.) Why does the NAMD 2.6 final result not coincide with the one in
the FEP tutorial?
2.) Why does the NAMD 2.7b1 lambda vs. dG curve look so strange, and
is the result valid in spite of this?
Thanks in advance.
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