**From:** Sadegh Faramarzi Ganjabad (*safaramarziganjabad_at_mix.wvu.edu*)

**Date:** Fri Oct 06 2017 - 14:04:39 CDT

**Next message:**Brian Radak: "Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation"**Previous message:**Chitrak Gupta: "Re: NAMD on Stampede 2"**In reply to:**Brian Radak: "Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation"**Next in thread:**Brian Radak: "Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation"**Reply:**Brian Radak: "Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Brian,

Thanks replying.

1) Regarding bonded terms, I thought they are already included; in the log

files I have these lines

FEP CURRENT LAMBDA VALUE 0

Info: FEP ELEC. ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND

LAMBDA = 0.5

Info: FEP ELEC. ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0.5 AND

LAMBDA = 1

Info: FEP VDW ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND

LAMBDA = 1

Info: FEP VDW ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND

LAMBDA = 1

Info: FEP BOND ACTIVE FOR ANNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND

LAMBDA = 1

Info: FEP BOND ACTIVE FOR EXNIHILATED PARTICLES BETWEEN LAMBDA = 0 AND

LAMBDA = 1

****

FEPTITLE: TS BOND2 ELECT2 VDW2

****

FEP: 0 22006.7270 -93162.0780 2413.1778

*****

If not, how could I include them?

2) How necessary it is to compute a difference in relative solvation free

energies?

3) Is there a way I could do study long time behavior of the BAR estimate

of the cumulative data with the ParseFEP plugin? I assume I should split

the entire simulation to smaller fractions?

Best,

Sadegh

On Thu, Oct 5, 2017 at 4:30 PM, Brian Radak <bradak_at_anl.gov> wrote:

*> Does your transformation also include bonded terms? You will not compute a
*

*> relative ionization free energy if you do not include those terms, although
*

*> you can, in principle, compute a difference in relative solvation free
*

*> energies by doing the corresponding calculation in the gas phase. I don't
*

*> know your reasons for running your simulation, but I feel that I should
*

*> point this out -- there are new keywords as of NAMD 2.11 for doing this
*

*> (see the user guide).
*

*>
*

*> Agreement between the forward and backward FEP calculations is only a
*

*> necessary condition for FEP convergence -- it is neither a sufficient
*

*> condition for convergence nor a meaningful condition for other estimators,
*

*> such as BAR.
*

*>
*

*> Another necessary, but still not sufficient, condition for convergence
*

*> might be found in the long time behavior of the BAR estimate of the
*

*> cumulative data (i.e. use the first 10 ns, then the first 20 ns, etc. and
*

*> see if the answer changes as the simulation gets longer).
*

*>
*

*> The forward and backward construction loses all meaning when analyzing
*

*> with thermodynamic integration, for the same reason as it does for BAR.
*

*>
*

*> HTH,
*

*> Brian
*

*>
*

*> On 10/05/2017 02:36 PM, Sadegh Faramarzi Ganjabad wrote:
*

*>
*

*>> Hello,
*

*>>
*

*>> I am running a test FEP simulation to calculate free energy of the
*

*>> ionization of an amino acid inside a membrane protein. Here is the FEP part
*

*>> of my namd config.
*

*>>
*

*>> source ../tools/fep.tcl
*

*>>
*

*>> alch on
*

*>> alchType FEP
*

*>> alchFile all-ion-beta.pdb
*

*>> alchCol B
*

*>> alchOutFile forward-shift-pr.fepout
*

*>> alchOutFreq 10
*

*>> alchBondDecouple on
*

*>> alchBondLambdaEnd 1.0
*

*>>
*

*>> alchVdwLambdaEnd 1.0
*

*>> alchElecLambdaStart 0.5 #soft potential
*

*>> alchVdWShiftCoeff 6.0
*

*>> #alchDecouple off
*

*>>
*

*>> alchEquilSteps 100
*

*>> set numSteps 500
*

*>>
*

*>> runFEPmin 0.0 1.0 0.0625 10000 1000 310
*

*>>
*

*>> Then I used ParseFEP of VMD. The difference between DeltaG of the forward
*

*>> and backward transformation is about 5 kcal/mol for lambda=0 to 0.5, and it
*

*>> become almost 0 for lambda = 0.6 to 1. I should probably increase
*

*>> simulation time for each lambda from 10,000 to say 10,000,000 until the
*

*>> plots of forward and backward lie on top of each other. My question is that
*

*>> is this the only criterion for convergence of FEP calculation? How can I
*

*>> make sure my simulation is long enough?
*

*>>
*

*>> Also, if I use thermodynamic integration method for free energy
*

*>> calculations, what would be convergence criteria for that?
*

*>>
*

*>> Thanks,
*

*>> Sadegh
*

*>>
*

*>>
*

*> --
*

*> Brian Radak
*

*> Postdoctoral Appointee
*

*> Leadership Computing Facility
*

*> Argonne National Laboratory
*

*>
*

*> 9700 South Cass Avenue, Bldg. 240
*

*> Argonne, IL 60439-4854
*

*> (630) 252-8643
*

*> brian.radak_at_anl.gov
*

*>
*

**Next message:**Brian Radak: "Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation"**Previous message:**Chitrak Gupta: "Re: NAMD on Stampede 2"**In reply to:**Brian Radak: "Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation"**Next in thread:**Brian Radak: "Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation"**Reply:**Brian Radak: "Re: convergence criterion of free energy perturbation (FEP) simulations for pKa calculation"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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