[gmx-users] Doubt about Free Energy Calculations using g_bar

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

I was interested in the process *prior* to the free energy change is carried out, before we carry out simulations pertaining to couple-lambda0 = vdw and couple-lambda1 = none. Hence, I am curious as to *how* the charges are set to zero in the topology for the ligand and if is it necessary in Gromacs 5.0 version.

For the Protein-ligand system, the tutorial suggests: (for version 5.0)
couple-lambda0          = none
couple-lambda1          = vdw-q
vdw_lambdas             = 0.00 0.05 0.10 ... 1.00 1.00 1.00 ... 1.00
coul_lambdas            = 0.00 0.00 0.00 ... 0.00 0.05 0.10 ... 1.00

So, if this is done, is it necessary to set the charges zero in topology for the ligand? If yes, can you please suggest me as to how can we do that using the index file and topology file?

-Bhagyesh

----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Friday, June 9, 2017 2:40:38 AM
Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar

On 6/8/17 11:46 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear all,
> 
> I am attempting to find Binding affinity of a Protein-ligand system by following the Free Energy tutorials (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/index.html).
> It says : "The procedure in this tutorial essentially assumes that charges have been properly been turned off prior to this point". How do we turn off the charges of a group specified in an index file (the ligand in my case) ?
> 

Either set them to zero in the topology or define couple-lambda0 = vdw and 
couple-lambda1 = none.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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