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

**Date:** Mon Nov 18 2013 - 11:44:59 CST

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Hello all,

I think I figured out the answers

The column before temperature is the average change in potential energy

(deltaUavg) and the column preceding it is the change in potential energy

(delta U). So I should calculate the variance of delta U values to optimize

delta lambda, length of each window?

Could some one confirm this?

thanks,

Shyno

On Fri, Nov 15, 2013 at 4:02 PM, Shyno Mathew <sm3334_at_columbia.edu> wrote:

*> 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)
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*>
*

*>
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*> #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
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*> 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
*

*>
*

*>
*

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

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