The large magnitudes of orthogonal barriers in such systems will lead to both
systematic and statistical
sampling errors that motivate the application of both approaches, preferably
repeated a few times each.
So I think that Justin is right, in an idealized situation. I might modify his
statement to indicate that the actual
(converged) free energy is a state function, but the estimate of the free
energy that you obtain from finite-time
simulations may well depend on the methodological approach. Using multiple
methodological approaches and
initial conformations is a good way to ensure convergence or to identify
sampling errors.
Chris.
-- original message --
>
>
> I have a question regards to PMF:
>
> Consider we are sure one protein will bind to membrane after 100ns in MD run
> and make a complex. Instead of pulling protein to membrane to calculate PMF,
> can we start from last configuration of protein-membrane complex and pull
> out protein to separate them and calculate the PMF?
>
>
>
> What would be the difference?
>
>
DeltaG is a state function; the direction is irrelevant. Keeping the sign
consistent with the final and initial states is the only thing that really
matters.
-Justin
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