[gmx-users] Gibbs free energy of binding

[mohsen ramezanpour]

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?



On Wed, Oct 20, 2010 at 2:28 PM, Justin A. Lemkul <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>> 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
>
> ========================================
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