[gmx-users] Re: free energy calculations

[Ragothaman Yennamalli]

>
>
> Message: 1
> Date: Tue, 05 Jul 2011 19:14:04 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] free energy calculations
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4E139ABC.1030107 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Ragothaman Yennamalli wrote:
> > Hi,
> > I want to run free energy calculations on a particular protein-ligand
> > complex. I do not have much knowledge on this so I have some questions,
> > hopefully someone might give me clear answers.
> > I am following the tutorial given in this link:
> >
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/08_advanced.html
> >
> > My questions are as follows:
> > 1. I am assuming that I do not need the "protein without the ligand"
> > form for free energy calculations. Am I right?
> >
>
> Free energy calculations can be done on a number of systems.  The tutorial
> is
> just one simple example.
>

Thanks for the mail. So, I technically do not need both the un-complexed and
complexed form of the protein with the ligand.

>
> > 2. To use g_bar, I need to run the protein-ligand complex with
> >     a) first with lambda ranging from 0.5 to 1 for vdw coupling and
> >     b) followed by lambda ranging from 0.5 to 1 for coulombic coupling
> > Adding these would give the deltaG I am looking for. Am I right?
> >
>
> No.  The range for lambda should be 0 to 1.  Using 0.5 to 1 gives only part
> of
> the free energy for the transformation, and not necessarily half.
>

Apologies, I should have mentioned as from 0 to 1. So, the first step is to
do vdw coupling followed by coulombic coupling. Right?

>
> > 3. Are there any papers that use g_bar function in gromacs to calculate
> > free energy?
> >
>
> The g_bar tool is relatively new to Gromacs, so maybe not.  The BAR method
> itself has been around for decades though, so its applications have been
> demonstrated in the literature many times.
>

Thanks for pointing this.
Raghu

>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
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