**From:** Nassar, Omneya (*omnassar_at_UTMB.EDU*)

**Date:** Sat Jul 21 2018 - 07:58:40 CDT

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Thank you Jerome for your prompt response. If you could further answer this question, I will greatly appreciate it. So at FEP lambda 0.0625 to 0.125, if I have 0,0 for alchVdwLambdaEnd, alchElecLambdaStart, respectively, do I have the geometry of NADH and ADP present or do I have the geometry of the intermediate at 0.0625 to 0.125?

Thanks!

Omneya

On Jul 21, 2018, at 6:02 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr<mailto:jerome.henin_at_ibpc.fr>> wrote:

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<mailto:omnassar_at_utmb.edu>> wrote:

Hello NAMD staff,

I am trying to properly implement the dual topology paradigm in Free Energy Perturbation technique for a mutation of NADH to ADP. I want to calculate two things: 1) the van der Waals free energy of NADH changing to ADP and 2) the electrostatics of NADH changing to ADP. Thus, I should have values for dGvdw and dGelec from two separate simulations. However, after reading over the documentation (http://www.ks.uiuc.edu/Research/namd/2.7/ug/node53.html

However, in contrast to my understanding of the above documuntation and according to this very general response (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2010-2011/1722.html

____________________________________________________________

VANDERWAALS CALCULATION/SIMULATION:

alch on

alchType FEP

alchFile N3A_ion.fep

alchCol B

alchOutFile $outname.fepout

alchOutFreq 500

alch on

alchType FEP

alchFile N3A_ion.fep

alchCol B

alchOutFile $outname.fepout

alchOutFreq 500

runFEP 0.6875 0.71875 0.03125 $numSteps

Your help is invaluable and I really appreciate your response.

Omneya Nassar

PhD Candidate in Pharmacology and Toxicology

University of Texas Medical Branch

301 University Blvd

Galveston, TX 77555

E-mail: omnassar_at_utmb.edu<mailto:omnassar_at_utmb.edu>

Phone: 409.772.0731

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