Yes, I missed the two terms, the solute entropy and solvent entropy. It is
certainly not a good practice to estimate the entropies at a diff temps with
a traj created at some other temp. Provided simulation has been run "long
enough", it should capture all relevant conformations with significant
population at that temp, however, as mentioned, REMD can make life much
easier.
On Mon, Sep 20, 2010 at 10:04 PM, Thomas Cheatham <tec3.utah.edu> wrote:
>
> > I'm trying to run mm-pbsa at different temperatures to analyze the
> > effects of temperature on the binding of a protein-DNA complex. I was
> > wondering if there is a way to specify the running temperature as a
> > parameter for the mm-pbsa script. I tried to set the temp variable to
> > the desired temperature, but it seems there is no effect. I am using
> > the mm-pbsa perl scripts with amber 10.
>
> No effect, seems correct to me. I would not expect much of an effect in
> mm-pbsa. Remember,
>
> deltaG = deltaH - T deltaS
>
> There is no temperature dependence to the "H" (loosely equivalent to the
> potential energy in the MD). Where temperature has an effect is in the
> entropy term which is solute entropy (via nmode or other estimates which
> may not even be turned on in your mm-pbsa analysis since it tends to be
> expensive) and potentially the solvation free energy term although this is
> likely small in a continuum approximation...
>
> It is highly unlikely you will be able to get temperature dependence from
> a single trajectory at 300K since at higher temperatures a larger ensemble
> of conformations would be sampled (meaning higher entropy and sampling of
> higher potential energy structures). To get the temperature dependence,
> likely a replica-exchange approach (at minimum) would be required...
>
> --tec3
>
>
>
>
>
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Received on Mon Sep 20 2010 - 19:30:05 PDT
