[gmx-users] RE: Gibbs free energy of binding

[mohsen ramezanpour]

reading your idea:
it seems to me I can't ignore entropy contribution because  my simulation is
at room tempreture.
Really I couldn't understand what can I do!
I am working at room tempreture and I want to estimate binding free
energy(delta G),can I ignore entropy in this simulation and calculate
binding free energy by the method that I said in my last email?
what do you think?
thank in advance for  your guid

On Thu, Oct 21, 2010 at 10:45 PM, mohsen ramezanpour <
ramezanpour.mohsen at gmail.com> wrote:

> reading your idea:
> it seems to me I can't ignore entropy contribution because  my simulation
> is at room tempreture.
> Really I couldn't understand what can I do!
> I am working at room tempreture and I want to estimate binding free
> energy(delta G),can I ignore entropy in this simulation and calculate
> binding free energy by the method that I said in my last email?
> what do you think?
> thank in advance for  your guid
>
>
>
> On Thu, Oct 21, 2010 at 12:15 PM, David van der Spoel <
> spoel at xray.bmc.uu.se> wrote:
>
>> On 2010-10-21 10.39, Ehud Schreiber wrote:
>>
>>> Actually, I believe that using the energy difference, Delta E, as an
>>> approximation to the free energy difference, Delta G, is a valid
>>> approach (which I'm considering myself). The entropic contribution to
>>> Delta G, namely -T Delta S, may be less prominent than Delta E.
>>> In addition, Delta S can be approximated by various means - see e.g.
>>> Doig&  Sternberg 1995. I understand that such an approach is utilized in
>>> the Accelrys Discovery Studio.
>>> Obviously, this is an approximation that might be too crude for some
>>> applications.
>>>
>>
>> As a simple example the hydrophobic effect at room temperature is largely
>> due to the entropy of the water [ at high temp it is due to the enthalpy of
>> the water ].
>>
>> Since the hydrophobic effect is involved in all ligand binding it seems
>> quite hopeless to get any reliable numbers when neglecting entropy. No
>> referee will buy that - I wouldn't.
>>
>>
>>
>>> What do you think?
>>>
>>> ------------------------------------------------------------------------
>>> --
>>>
>>> On Oct 21, 2010, at 09:25 , Sander Pronk wrote:
>>>
>>> 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?
>>>>
>>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>>
>> --
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>
>
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