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

**Date:** Mon Nov 18 2013 - 23:21:35 CST

**Next message:**Chan Tabris C: "Compile NAMD with FFTW3 and MPI"**Previous message:**JÃ©rÃ´me HÃ©nin: "Re: FEP calculations: optimizing the dlambda, number of steps"**In reply to:**JÃ©rÃ´me HÃ©nin: "Re: FEP calculations: optimizing the dlambda, number of steps"**Next in thread:**JÃ©rÃ´me HÃ©nin: "Re: FEP calculations: optimizing the dlambda, number of steps"**Reply:**JÃ©rÃ´me HÃ©nin: "Re: FEP calculations: optimizing the dlambda, number of steps"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello Jerome,

thanks so much for your reply.

I am trying to calculate the variance of delta U values to optimize delta

lambda, length of each window as discussed in the following paper:

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

(page 10242 of article)

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). Is this correct?

thanks again,

Shyno

On Mon, Nov 18, 2013 at 6:32 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

*> Hi,
*

*>
*

*> AlchDecouple only makes a difference if there are nonbonded interactions
*

*> within the perturbed groups.
*

*>
*

*> "AlchDecouple on" means that these interactions are unperturbed, so that
*

*> the "intact" molecule is decoupled from its environment.
*

*> "AlchDecouple off" means that the molecule's nonbonded interactions
*

*> (included its self-interactions) are perturbed.
*

*>
*

*> Jerome
*

*>
*

*>
*

*> ----- Original Message -----
*

*> > 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
*

*> >
*

*>
*

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

**Next message:**Chan Tabris C: "Compile NAMD with FFTW3 and MPI"**Previous message:**JÃ©rÃ´me HÃ©nin: "Re: FEP calculations: optimizing the dlambda, number of steps"**In reply to:**JÃ©rÃ´me HÃ©nin: "Re: FEP calculations: optimizing the dlambda, number of steps"**Next in thread:**JÃ©rÃ´me HÃ©nin: "Re: FEP calculations: optimizing the dlambda, number of steps"**Reply:**JÃ©rÃ´me HÃ©nin: "Re: FEP calculations: optimizing the dlambda, number of steps"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Tue Dec 31 2013 - 23:24:00 CST
*