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

[Varvdekar Bhagyesh Rajendra]

Dear Mark,

Unless I'm mistaken, even though they are non-physical states and do not exist in reality, they have the required modification in the actual physical state (precisely, the non bonded interaction between protein and ligand) that I actually need and I wish to use the same and do Normal mode calculations to study the effect of the said perturbation at each lambda from 0 to 1.

I would appreciate any suggestions to undertake the above quest.

Best Regards,

Bhagyesh

----- Original Message -----
From: "Mark Abraham" <mark.j.abraham at gmail.com>
To: gmx-users at gromacs.org
Sent: Sunday, June 11, 2017 9:22:51 PM
Subject: Re: [gmx-users] Doubt about Free Energy Calculations using g_bar

Hi,

To what end? These are non-physical states.

Mark

On Sun, 11 Jun 2017 16:28 Varvdekar Bhagyesh Rajendra <
bhagyesh.varvdekar at research.iiit.ac.in> wrote:

> 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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