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

**Date:** Tue Jul 24 2018 - 02:55:40 CDT

**Next message:**Nassar, Omneya: "Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately?"**Previous message:**Kowsar Khajeh: "velocity.pdb and velocity unit in NAMD"**Maybe in reply to:**Jérôme Hénin: "Re: 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?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

With alchVdwLambdaEnd=0 all atoms (outgoing and incoming groups) will be

coupled to the environment at all times through the Lennard-Jones potential

(lambda_LJ = 1).

I'm now realizing that the transformation you had in mind doesn't work,

because it won't sum to the total mutation free energy. What you can do is

a series of three simulations:

1 - discharge group A with only LJ of A present

2 - vanish LJ of A while growing LJ of B

3 - charge group B with only LJ of B present

Then the sum of free energies from steps 1 and 3 will give you an idea of

the electrostatic contribution, and step 2 gives the vdW part.

Jerome

On Tue, 24 Jul 2018 at 02:54, Nassar, Omneya <omnassar_at_utmb.edu> wrote:

*> You are correct; my question is more complex. I am asking about the
*

*> outgoing and incoming atoms for the alchemical transformation when I have
*

*> alchVdwLambdaEnd=0 and alchElecLambdaStart=0. So for my system, I am
*

*> starting with NADH and transforming it to ADP. At the first window (0/32 to
*

*> 1/32), does the simulation only use the NADH van der waals shape and
*

*> charges while ignoring ADP’s shape for the Free Energy calculation or is
*

*> the shape of both NADH and ADP used in the calculation and only the charges
*

*> of NADH are used for the simulation?
*

*>
*

*> Attached is a diagram of what I am asking. If it is still confusing,
*

*> please let me know. I really appreciate your patience and thanks again for
*

*> helping me.
*

*>
*

*>
*

*>
*

*> Omneya
*

*>
*

*>
*

*>
*

*> *From: *Jérôme Hénin <jerome.henin_at_ibpc.fr>
*

*> *Sent: *Monday, July 23, 2018 4:15 PM
*

*> *To: *Nassar, Omneya <omnassar_at_UTMB.EDU>
*

*> *Cc: *Namd Mailing List <namd-l_at_ks.uiuc.edu>
*

*> *Subject: *Re: namd-l: Dual Topology in FEP Calculations - How to
*

*> Calculate Electrostatics and van der Waals Free Energies Separately?
*

*>
*

*>
*

*>
*

*> All particles are present at all times; their interactions vary. I think
*

*> there was more to your question, but I didn't get it.
*

*>
*

*>
*

*>
*

*> Jerome
*

*>
*

*>
*

*>
*

*> On Sat, 21 Jul 2018 at 14:59, Nassar, Omneya <omnassar_at_utmb.edu> wrote:
*

*>
*

*> 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> 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> 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
*

*> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__na01.safelinks.protection.outlook.com_-3Furl-3Dhttp-253A-252F-252Fwww.ks.uiuc.edu-252FResearch-252Fnamd-252F2.7-252Fug-252Fnode53.html-26data-3D02-257C01-257Comnassar-2540UTMB.EDU-257C099dbcc3f2c0496789c708d5eef97f81-257C7bef256d85db4526a72d31aea2546852-257C0-257C1-257C636677677711073805-26sdata-3DahfoJSCH4i7e6sVP6dY4rWsBU5WB372Idz9USilrGXE-253D-26reserved-3D0%26d%3DDwMFaQ%26c%3DOCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag%26r%3DjUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc%26m%3Dojx3DcDQE2hr2yiIPoSjDlagDXtFEW9J1hoRZUO6cVc%26s%3DiFIxvgyH8sawhze2_wMWmonbVfmpzGFOA8R3KlI9fgk%26e%3D&data=02%7C01%7Comnassar%40UTMB.EDU%7Cdfc37453346e4ab070bd08d5f0e16c7b%7C7bef256d85db4526a72d31aea2546852%7C0%7C0%7C636679773341569223&sdata=ovmkZX%2B6ciRgIIeBp%2FzVWFEPG28gn2iJqlLZZ5w8Kcc%3D&reserved=0>),
*

*> it seems that it is not possible to properly separate van der Waals and
*

*> electrostatics calculations using FEP.
*

*>
*

*> 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
*

*> <https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__na01.safelinks.protection.outlook.com_-3Furl-3Dhttp-253A-252F-252Fwww.ks.uiuc.edu-252FResearch-252Fnamd-252Fmailing-5Flist-252Fnamd-2Dl.2010-2D2011-252F1722.html-26data-3D02-257C01-257Comnassar-2540UTMB.EDU-257C099dbcc3f2c0496789c708d5eef97f81-257C7bef256d85db4526a72d31aea2546852-257C0-257C1-257C636677677711073805-26sdata-3DWOaQxK6X-252B038lGSGPbfUnswBbf0vH7-252Bwp-252Ffqfr42-252B74-253D-26reserved-3D0%26d%3DDwMFaQ%26c%3DOCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag%26r%3DjUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc%26m%3Dojx3DcDQE2hr2yiIPoSjDlagDXtFEW9J1hoRZUO6cVc%26s%3D9dY63UuQAwNwG25E8c_uCCkkkQg-oVhpS_0XGIMXKjM%26e%3D&data=02%7C01%7Comnassar%40UTMB.EDU%7Cdfc37453346e4ab070bd08d5f0e16c7b%7C7bef256d85db4526a72d31aea2546852%7C0%7C0%7C636679773341579232&sdata=9MVdvK6kjkvEt2TmdQHc8LK%2BwknzcMlsDGvGc9XE%2BfU%3D&reserved=0>),
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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).
*

*>
*

*> ____________________________________________________________
*

*> VANDERWAALS CALCULATION/SIMULATION:
*

*>
*

*> # FEP PARAMETERS
*

*>
*

*> source fep.tcl
*

*>
*

*> alch on
*

*> alchType FEP
*

*> alchFile N3A_ion.fep
*

*> alchCol B
*

*> alchOutFile $outname.fepout
*

*> alchOutFreq 500
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*>
*

*> alchVdwLambdaEnd 1.0
*

*> alchElecLambdaStart 1.0
*

*> alchVdWShiftCoeff 5.0
*

*> alchDecouple on
*

*> alchEquilSteps 1000
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*> set numSteps 6251000
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*>
*

*>
*

*> runFEP 0.6875 0.71875 0.03125 $numSteps
*

*> ______________________________________________________________
*

*> ELECTROSTATICS CALCULATION/SIMULATION:
*

*>
*

*> # FEP PARAMETERS
*

*>
*

*> source fep.tcl
*

*>
*

*> alch on
*

*> alchType FEP
*

*> alchFile N3A_ion.fep
*

*> alchCol B
*

*> alchOutFile $outname.fepout
*

*> alchOutFreq 500
*

*>
*

*> alchVdwLambdaEnd 0.0
*

*> alchElecLambdaStart 0.0
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*> alchVdWShiftCoeff 5.0
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*> alchDecouple on
*

*> alchEquilSteps 1000
*

*> set numSteps 6251000
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*>
*

*>
*

*> runFEP 0.6875 0.71875 0.03125 $numSteps
*

*>
*

*> Using the input examples above, am I properly separating electrostatics
*

*> and van der waals calculations? If so, how is the geometry of the molecule
*

*> affected when I run the electrostatics calculation? Do I have both NADH and
*

*> ADP present geometrically, but only the charges are changing?
*

*>
*

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

*>
*

*> Thank you!
*

*>
*

*> 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
*

*> Phone: 409.772.0731
*

*>
*

*>
*

*>
*

**Next message:**Nassar, Omneya: "Re: Dual Topology in FEP Calculations - How to Calculate Electrostatics and van der Waals Free Energies Separately?"**Previous message:**Kowsar Khajeh: "velocity.pdb and velocity unit in NAMD"**Maybe in reply to:**Jérôme Hénin: "Re: 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?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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