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

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

Just so we are on the same page, this means that if I don't touch the topology file and use the following mdp snippet, charges *are present* in the topology file for the ligand group and they are automatically set to zero while turning on vdW interactions (from 0 to 1) right ? Hence, there is no need to manually set charges to zero (The old style of doing the calculations), right?.

Then the charges too, are turned off from 0 to 1? (1 state being the actual charges present in the topology file).


Thank you,

Bhagyesh

----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Saturday, June 10, 2017 5:12:25 AM
Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar

On 6/8/17 6:14 PM, Varvdekar Bhagyesh Rajendra wrote:
> 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.
> 

You don't have to change anything in the topology.  Editing it to set charges to 
zero is an old style of doing these calculations.

> 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?
> 

Don't touch the topology.  Index files don't do any good here, anyway.  They're 
for selections in analysis or various groups during MD.  What the above .mdp 
settings do is turn on vdW interactions before turning on charges, which is 
necessary for stability.

-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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