From: Shyno Mathew (sm3334_at_columbia.edu)
Date: Mon Nov 18 2013 - 12:56:19 CST
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,
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?
> 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
>> 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 minimization?
>> 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
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