**From:** Jérôme Hénin (*jerome.henin_at_ibpc.fr*)

**Date:** Sat Jul 21 2018 - 05:58:02 CDT

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Dear Omneya,

Your simulation parameters seem correct to me, as does your understanding

of the alchemical process in this implementation.

Best,

Jerome

On Fri, 20 Jul 2018 at 22:07, Nassar, Omneya <omnassar_at_utmb.edu> wrote:

*> Hello NAMD staff,
*

*>
*

*> I am trying to properly implement the dual topology paradigm in Free
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*> Energy Perturbation technique for a mutation of NADH to ADP. I want to
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*> calculate two things: 1) the van der Waals free energy of NADH changing to
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*> ADP and 2) the electrostatics of NADH changing to ADP. Thus, I should have
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*> values for dGvdw and dGelec from two separate simulations. However, after
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*> reading over the documentation (
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*> http://www.ks.uiuc.edu/Research/namd/2.7/ug/node53.html), it seems that
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*> it is not possible to properly separate van der Waals and electrostatics
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*> calculations using FEP.
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*>
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*> However, in contrast to my understanding of the above documuntation and
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*> according to this very general response (
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*> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2010-2011/1722.html),
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*> it is claimed that it is possible to separate vanderwaals and
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*> electrostatics.
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*>
*

*> Below is the input for van der Waals and electrostatics for each lambda
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*> value (I am simulating each lambda window independently).
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*>
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*> ____________________________________________________________
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*> VANDERWAALS CALCULATION/SIMULATION:
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*>
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*> # FEP PARAMETERS
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*>
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*> source fep.tcl
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*>
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*> alch on
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*> alchType FEP
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*> alchFile N3A_ion.fep
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*> alchCol B
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*> alchOutFile $outname.fepout
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*> alchOutFreq 500
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*>
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*> alchVdwLambdaEnd 1.0
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*> alchElecLambdaStart 1.0
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*> alchVdWShiftCoeff 5.0
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*> alchDecouple on
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*> alchEquilSteps 1000
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*> set numSteps 6251000
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*>
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*>
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*> runFEP 0.6875 0.71875 0.03125 $numSteps
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*> ______________________________________________________________
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*> ELECTROSTATICS CALCULATION/SIMULATION:
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*>
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*> # FEP PARAMETERS
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*>
*

*> source fep.tcl
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*>
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*> alch on
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*> alchType FEP
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*> alchFile N3A_ion.fep
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*> alchCol B
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*> alchOutFile $outname.fepout
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*> alchOutFreq 500
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*>
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*> alchVdwLambdaEnd 0.0
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*> alchElecLambdaStart 0.0
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*> alchVdWShiftCoeff 5.0
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*> alchDecouple on
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*> alchEquilSteps 1000
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*> set numSteps 6251000
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*>
*

*>
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*> runFEP 0.6875 0.71875 0.03125 $numSteps
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*>
*

*> Using the input examples above, am I properly separating electrostatics
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*> and van der waals calculations? If so, how is the geometry of the molecule
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*> affected when I run the electrostatics calculation? Do I have both NADH and
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*> ADP present geometrically, but only the charges are changing?
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*>
*

*> Your help is invaluable and I really appreciate your response.
*

*>
*

*> Thank you!
*

*>
*

*> Omneya Nassar
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*> PhD Candidate in Pharmacology and Toxicology
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*> University of Texas Medical Branch
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*> 301 University Blvd
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*> Galveston, TX 77555
*

*> E-mail: omnassar_at_utmb.edu
*

*> Phone: 409.772.0731
*

*>
*

*>
*

**Next message:**Jérôme Hénin: "Re: ABF Questions"**Previous message:**Giacomo Fiorin: "Re: [NAMD] Define time-dependent grid force"**In reply to:**Nassar, Omneya: "Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately?"**Next in thread:**Nassar, Omneya: "Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately?"**Reply:**Nassar, Omneya: "Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately?"**Maybe reply:**Jérôme Hénin: "Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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