[gmx-users] Gibbs free energy of binding
mohsen ramezanpour
ramezanpour.mohsen at gmail.com
Thu Oct 21 09:18:12 CEST 2010
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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
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