From: Floris Buelens (floris_buelens_at_yahoo.com)
Date: Fri Jun 19 2009 - 02:39:05 CDT
The T in both kTs should be the target temperature for the ensemble. If you set the output frequency to 1 you should be able to recover exactly the dG value reported by NAMD using the FEP formula.
However your question does make me wonder why the original FEP coder thought it useful to state the instantaneous temperature on every line of the FEP output file, since this value is not used in the calculation...?
----- Original Message ----
From: Michael Thomas <exploding.dinosaurs_at_gmail.com>
Sent: Wednesday, 17 June, 2009 12:51:31
Subject: namd-l: How is dG caluclated from dE during FEP?
I am trying to work out how the calculation of dG has been implemented in a FEP calculation. So far I have assumed that
dG = -k.T(avg).ln<exp[-dE/(kT(inst)]> where T(avg) is the average temperature over a lambda window and T(inst) is the instantaneous temperature, but the values of dG are still a bit off.
Thankyou for your help
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