**From:** Brian Radak (*bradak_at_anl.gov*)

**Date:** Thu Oct 05 2017 - 15:30:28 CDT

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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
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*>
*

*> 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

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