AMBER Archive (2008)

Subject: Re: AMBER: convergence of free energy calculations

From: David Mobley (dmobley_at_gmail.com)
Date: Thu Jan 24 2008 - 12:20:35 CST

There is no absolute way to know if something is converged. To use an
analogy, no matter how long you explore a particular valley when
hiking, there's no way of knowing if the next valley is deeper until
you go over there and check. Similarly, you can never be sure you're
seen all the relevant conformations when doing free energy
calculations (or any other sort of simulations) -- there could always
be another valley you haven't looked in yet.

Some things you can do that can help diagnose convergence:
(1) Ensure you get the same results beginning from substantially
different starting conformations
(2) Ensure standard metrics like RMSD, energy, number of hydrogen
bonds, etc., have stopped drifting
(3) Use a automatic convergence detection approach like Wei Yang's
reverse cumulative averaging (pub in JCP from the Karplus group in the
last few years)

and various others, of course.

David Mobley
UCSF
http://www.dillgroup.ucsf.edu/~dmobley

On Jan 22, 2008 3:54 AM, saurabh agrawal <imsam100_at_yahoo.co.in> wrote:
> Dear Amber Users,
>
> May anyone tell me, what is the meaning of convergence of the free energy
> calculations? Is there any way to know that energy calculations are
> conserved or not?
>
> Further I want to make a plot for free energy of each snapshot used for
> MM_PBSA calculations. How can I do this? Is there any script or program
> required to calculate energy for each snap separately?
>
> I shall be highly thankful to every one, how can give me suggestions in
> this regards.
>
> saurabh
>
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