**From:** Shyno Mathew (*sm3334_at_columbia.edu*)

**Date:** Fri Nov 15 2013 - 15:02:06 CST

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Dear all,

I am doing the FEP calculations and need some help in understanding the

.fepout file.

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

results.

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?

http://pubs.acs.org/doi/abs/10.1021/jp102971x

(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

minimization?

thanks,

Shyno

-- Shyno Mathew PhD student Department of Chemical Engineering Columbia University

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