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

[Mark Abraham]

Hi,

On Sun, Jun 11, 2017 at 10:39 PM Varvdekar Bhagyesh Rajendra <
bhagyesh.varvdekar at research.iiit.ac.in> wrote:

> 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.
>

I expect that the numbers you seek will be computed. But you're also going
to scale down e.g. the ligand-solute interactions, and IMO it's unlikely
you'll observe anything that you can claim is insight into the physical
systems.

Mark


> 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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