From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Fri Nov 15 2013 - 15:02:06 CST
I am doing the FEP calculations and need some help in understanding the
1. this is the first part of .fepout file
# STEP Elec vdW dE dE_avg Temp dG
# l l+dl l l+dl E(l+dl)-E(l)
#NEW FEP WINDOW: LAMBDA SET TO 0 LAMBDA2 0.05
FepEnergy: 0 -469793 -469790 34401.03 34399.75 0.8153 0.8153 298.6998
0.8153 FepEnergy: 100 -472878 -472876 33902.44 33900.11 0.4059 0.3622
313.4741 0.1558 FepEnergy: 200 -472922 -472919 33338.32 33336.3 0.8862
0.1122 312.7195 -0.3716
I understand the penultimate column is temperature and the last column is
dG value. What exactly are the other columns?
2. I am trying to see what dlambda, number of steps will give me accurate
Following article says keeping the variance at each stage on the order of
1-2 KT usually guarantees good overlap between probability distributions in
two consecutive strata and a reliable error estimate.
Here the variance means the variance of dG values (only of the ensemble
average, not including minimization??) for a given lambda window?
(talking about page 10242 of article)
For 300 K, 1-2 KT is 0.596 - 1.192 Kcal/mol.
The variance (considering ensemble (not minimization values) dG values for
first window, lambd= 0 to lambda=0.05) is 0.0158. So it's one order lower.
This means I need to change dlambda and/or change the number of steps after
-- Shyno Mathew PhD student Department of Chemical Engineering Columbia University
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