FEP on 2.7b1

From: Christopher Hartshorn (cmhartshorn_at_wsu.edu)
Date: Mon May 11 2009 - 15:38:37 CDT

Hi all. I am now not sure what the default parameters are for NAMD
2.7b1 (MacOSX x86 executable) for the fep calculations. I originally
did several calculations right after the release of this build and
would like to know because the remaining calculations I have to
perform should use the same parameters (they are comparisons of dG's
of binding). I had originally run these with just "fep on" plus the
usual info on step size, fepout freq. etc. but not with any
specifications such as "decouple" or "fepElecLambdaStart" etc. I
would like to begin specifying in my config file these other
parameters so that I do not have this problem in the future thus the
reason I am asking. From what I have read, the defaults are usually:
fepElecLambdaStart 0.5
fepVdwLambdaEnd 1.0
decouple off

Is this correct for NAMD 2.7b1?

Also, if it is true that the decouple is off on mine then how
important is it to be using decoupling? In other words, should I redo
those calculations with the decouple on (if it was even off to begin
with) and continue the remaining ones with it on as well? Or if it
does not matter and it was off then continuing exactly as I ran it the
last time is what I will do. I am performing these on two sims (bound
and unbound) times four different types of ligands (each ligand
molecule is around 100 atoms). Thus, I am doing double annhilations
with ddG=dG1-dG (If this helps for the advice). Admittedly, the first
bound/unbound set I did so far with 2.7b1 default parameters has a ddG
which is extremely close to experimental values. So, I'm not sure if
I want to mess with a good thing or if it's more that just I got
lucky. Thank you again for any help.

Chris Hartshorn


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