[gmx-users] Gibbs free energy of binding

[mohsen ramezanpour]

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?
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?)
thanks in advance
Mohsen

On Tue, Oct 19, 2010 at 2:56 PM, Justin A. Lemkul <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 | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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