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

[Varvdekar Bhagyesh Rajendra]

Dear Justin,

Thank you for the valuable insight. 

While on the same subject, can you give any comments on the possibility of using the same Free energy code in Gromacs to scale the non bonded interactions between protein & ligand while simultaneously doing Normal Mode analysis on the scaled interaction conformation to study the effect of the scaled interactions.

If its not plausible in Gromacs, can you suggest any other software.

Best Regards,

Bhagyesh

----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Sunday, June 11, 2017 7:01:26 AM
Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar

On 6/10/17 6:15 AM, Varvdekar Bhagyesh Rajendra wrote:
> 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?.
> 

Yes.  You can easily confirm this using energygrps between your transformed 
molecule and the rest of the system.  Coul-SR should be zero.

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

Charges are turned *on* if they are defined as off in the A-state (lambda=0) and 
on in the B-state (lambda=1).

-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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