[gmx-users] Gibbs free energy of binding

Sander Pronk pronk at cbr.su.se
Thu Oct 21 09:25:16 CEST 2010 

Hi Mohsen,

The mean energy difference is only one component of the free energy difference. 

Before you go any further I'd suggest reading a good book on molecular simulations, like 'Understanding Molecular Simulations' by Frenkel and Smit. 

There's a good reason free energy calculations cover over half of that book.

Sander


On Oct 21, 2010, at 09:18 , mohsen ramezanpour wrote:

> Dear Justin
> 
> If I do  two  MD simulations for a short time in the same conditions(of course separately for protein and drug)
>  and calculate total energy of each one and sum them with each other as E1 as nonbonding free energy of system.
> then a MD simulation for Protein-drug system in the same condition and calculate it's total energy too as E2 as bound system .
> what does (E1-E2)mean?
> I think it is binding free energy,Is not it?
> in the other hand when we are working on NPT ensamble it means Gibbs free energy is the main energy and our total energy is equal to Gibbs free energy.
> Then,what is the problem?
> 
> 
> 
> 
> 
> On Wed, Oct 20, 2010 at 3:31 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 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
> 
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