Re: FEP implementation in NAMD 2.6 vs. 2.7b1

From: Floris Buelens (
Date: Wed Jul 29 2009 - 01:50:40 CDT

Hi Dan,

as a general principle it's dangerous to make presumptions about how the transformation pathway 'should' look, since a fundamental characteristic of the method is that your intermediate states bear no realtion to any physical reality, and as such it's only really valid to compare the readout at the end points with known values, and / or determine objective statistical measures of the validity of the transformation pathway (such as overlap between states or reproducibility). The new implementation will definitely produce a different-looking curve as the lambda-dependence of both van der Waals and electrostatics is very different from previous versions.



----- Original Message ----
From: Dan Bolintineanu <>
Sent: Tuesday, 28 July, 2009 23:50:37
Subject: namd-l: FEP implementation in NAMD 2.6 vs. 2.7b1

Hi all,

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
fepElecLambdaStart 0.5
fepVdwLambdaEnd 1.0
decouple on
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.

Dan Bolintineanu


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