[gmx-users] free energy calculations

[Justin A. Lemkul]

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.

> 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.

> 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.

-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

========================================