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

**Date:** Mon Nov 18 2013 - 12:56:19 CST

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also, can some one explain the parameter "AlchDecouple"

I have done runs with both " alchDecouple on" and "alchDecouple off", but

didn't notice any difference while plotting delta G vs. deltalambda values.

Any help will be really appreciated,

thanks,

Shyno

On Mon, Nov 18, 2013 at 12:44 PM, Shyno Mathew <sm3334_at_columbia.edu> wrote:

*> 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)
*

*>>
*

*>>
*

*>> #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
*

*>>
*

*>>
*

*>
*

*>
*

*> --
*

*> Shyno Mathew
*

*> PhD student
*

*> Department of Chemical Engineering
*

*> Columbia University
*

*>
*

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

**Next message:**Jérôme Hénin: "Re: FEP calculations: optimizing the dlambda, number of steps"**Previous message:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**In reply to:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**Next in thread:**Jérôme Hénin: "Re: FEP calculations: optimizing the dlambda, number of steps"**Reply:**Jérôme Hénin: "Re: FEP calculations: optimizing the dlambda, number of steps"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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