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

chris.neale at utoronto.ca chris.neale at utoronto.ca
Sun Oct 24 20:02:54 CEST 2010


Writing H as E+PV does not change the nature of my question. It was  
said that when computing binding Delta Delta G between two close  
variants, most entropic contributions would tend to cancel. My  
question is why, when there are many components to the gibbs free  
energy, would some components (stated as entropy) cancel in a delta  
delta G while some are not expected to cancel (implicitly taken to be  
enthalpy or internal energy or pressure volume work). And also, is  
this a hunch or has it been shown?


-- original message --

Dear Chris
Do you mean Gibbs free energy?
there are a general relation in statistical mechanics as below:
in this relation E is internal energy and S is entropy,then enthalepy is not
comming in relation anywhere,
besides there are not any reason for canceling G when Del Del S is canceled

On Sun, Oct 24, 2010 at 9:04 PM, <chris.neale at utoronto.ca> wrote:

> Ehud,
> when computing binding Delta Delta G between two close variants, why would
> entropy tend to cancel and enthalpy not tend to cancel? Even in the case of
> small perturbations, this sounds like wishful thinking to me ;)
> Chris.
> -- original message --
> Hi Moshen,
> I think everybody agrees that a full calculation such as Free Energy
> Perturbation is the accurate, if difficult and lengthy, approach.
> The entropic effects usually cannot simply be ignored. All I tried to
> say was that there are approximation schemes for these (see the
> reference below). Still, I would trust such approximations only when
> computing binding Delta Delta G between two close variants (e.g. a wild
> type protein and a one residue mutation) such that -

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