Re: [AMBER] alpha helical content as reaction coordinate

From: David Case <>
Date: Sun, 15 Jan 2017 13:52:42 -0500

On Sun, Jan 15, 2017, Bin Sun wrote:

> I want to study the PMF of a peptide (about 22 residues) folding precess
> using umbrella sampling method. Can I define a collective variable, alpha
> ( its value lies between 0 and 1 ) that could describe the a-helical
> content of this peptide and then use this alpha as the reaction coordinate ?

You *could* do this, but it would require both cleverness (to define the
appropriate collective variable), and coding effort (to incororate this into
the Amber codes.)

You should also expect considerable (enormous? intractable?) problems in
sampling. Configurations that have alpha=0.5 might have the first half
of the peptide folded and the second half unfolded; or vice versa; or the
first and last parts folded with the middle part unfolded, etc. It would
be very difficult to generate an equilibrated set of conformers in such a

You might consider temperature replica-exchange methods to interpolate between
folded and unfolded ensembles. Others on the list might have some good ideas
to point to as well.


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Received on Sun Jan 15 2017 - 11:00:03 PST
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