[gmx-users] Gibbs free energy of binding

[Justin A. Lemkul]

mohsen ramezanpour wrote:
> Dear Justin
> You are right,But I searched in tools and I found g_sham
> It is very useful tool for estimating Gibbs free energy,Enthalepy ,
> emtropy and ...
> I think I can use from that for my calculation of binding free energy(In 
> the other words,del G free energy of system )
> how do you think about g_sham?
> 
> 

It is not applicable.  g_sham simply determines free energies based on 
histograms of two independent variables.  PMF is the appropriate technique for 
what you want to do.  I can see no other effective way to conduct your study 
using Gromacs.

-Justin

> 
> On Wed, Oct 20, 2010 at 2:28 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     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>
>         <mailto: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> <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 <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

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