[gmx-users] PMF - Protein-Me​brane

Christopher Neale chris.neale at mail.utoronto.ca
Wed Aug 15 17:51:10 CEST 2012

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.


-- 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.


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