[gmx-users] Gibbs free energy of binding

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> Dear Gromacs users
> 
> I want to calculate Gibbs free energy too,but about Protein-drug binding.
> Please guide more clearly,what texts I need to read for learning how can 
> I do it?

Look into the literature and nearly any of the popular simulation textbooks.

> Besides,g-energy has an option for estimating free energy from 
> trajectory file(-fee option)
> I thought if I had a trajectory file of binding state I could estimate 
> binding free energy by this option.
> am  I right?
> does it give me Gibbs free energy?(Is this equall to binding free energy?)

Never used this option, but from the description of the option, it calculates 
delta(G) relative to an ideal gas state, which sounds completely unrelated to 
what you want to accomplish.

Besides, if g_energy could magically solve this difficult problem, no one would 
bother with more thorough methods, like PMF or thermodynamic integration.

-Justin

> thanks in advance
> Mohsen
> 
> On Tue, Oct 19, 2010 at 2:56 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     shahab shariati wrote:
> 
>         Hi gromacs users
>          Can I use gromacs for obtaining Gibbs free energy of binding of
>         protein and dna?
> 
> 
>     Yes.  I would suggest you read about potential of mean force
>     calculations.
> 
>     -Justin
> 
>     -- 
>     ========================================
> 
>     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
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
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-- 
========================================

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

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