[gmx-users] Re: free energy calculations
Justin A. Lemkul
jalemkul at vt.edu
Wed Jul 6 16:28:36 CEST 2011
Ragothaman Yennamalli wrote:
> Message: 1
> Date: Tue, 05 Jul 2011 19:14:04 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] free energy calculations
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4E139ABC.1030107 at vt.edu <mailto:4E139ABC.1030107 at vt.edu>>
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> 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
> > hopefully someone might give me clear answers.
> > I am following the tutorial given in this link:
> > 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.
This is discussed in the tutorial:
> > 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
> > 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?
No, the opposite. You do not want to remove vdW terms from charged species.
This topic is addressed in the tutorial.
> > 3. Are there any papers that use g_bar function in gromacs to
> > free energy?
> The g_bar tool is relatively new to Gromacs, so maybe not. The BAR
> itself has been around for decades though, so its applications have been
> demonstrated in the literature many times.
> Thanks for pointing this.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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