Re: [gmx-users] Re: A question about "PEF"

[zjim]

many thanks, mic
After youy explanation, i do understand "PMF" much better.
I think "PMF" may be useful for looking for the intermediate of two minimal conformations according to your explanation.
It is fortunately to learn "PMF" can be calculate in gromacs, then let me have a try!

Zhjim

>The potential of mean force is actually the free energy difference.
> between the states at the two well defined endpoints of an arbitrarily 
> defined reaction path.
> This "reaction path" can be, for example, the path traveled by a molecule
> in a solvent through a distance dz normal to a surface. The result would be 
> the free energy of adsorption if z(lambda_0) is a point well away from the
> surface and z(lambda_1) is the equilibrium distance of an adsorbed
> molecule. Other frequently used reaction paths are the path that
> an ion travels through a ion channel or the path defined by 
> a rotation trhough a dihedral angle in a molecule in solution.
> 
> The, maybe confusing, name PMF comes from the fact that the PMF is 
> customarily calculated as the integral of the average force as a function 
> of lambda going from lambda=0 to lambda=1, which in the above case would
> correspond to the two states defined by the molecule-surface distance
> z(lambda_0) and z(lambda_1)
> If you write the average force as <F> = <dU/dz>, put that expression
> in the integral and replace z by lambda you see that this is nothing elso 
> but a special case of a thermodynamic integration ... see, for example 
> textbooks such as Allen, Tildeslay for more detailed explanations.
> 
> You can calculate the PMF in gromacs with the pull code. Be careful
> though, in all but the newset version of Gromacs there seem to be a couple
> of bugs in the pull code.
> 
> mic
> 
> 
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