FEP on NAMD2.6 versus latest CVS NAMD build

From: Christopher Hartshorn (cmhartshorn_at_wsu.edu)
Date: Fri Jan 30 2009 - 00:54:54 CST

Hi all. I am running some tests to decide the optimal lambda
differences and nsteps. In the process I noticed that when running
the exact same system with the exact same FEP and config file
parameters, that I received totally different results between
precompiled NAMD 2.6 and the latest CVS build, that I compiled
myself. The difference is on the order 30 Kcal. Thus the reason I am
curious. Is there a difference between the two versions on how the
FEP calculation is performed? If there is then which values would I
trust? Old or new?
I might add that the reason for two different versions is that I have
access to a linux server (the precompiled NAMD is on this one) and we
have several individual 8-core Intel Macs which I found it better to
compile myself. Thus, why I am curious because if one is more
accurate I will need to compile for the server or revert the Macs to
ver.2.6.

Thank you for any help

Chris Hartshorn
WSU

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