Re: inconsistency in ABF results for helix unfolding

From: gmail (
Date: Wed Jan 28 2015 - 03:49:54 CST


I think that in free energy calculations, choosing a good collective variable is usually more important than the method used (which more or less all suffer from the same problems). Sampling is obviously the second big issue.

It seems you used end to end distance as a collective variable, which does not strike me as the best choice. The peptide could be unfolded and still have a short end to end distance. On the other hand, a shorter end to end distance does not mean that the peptide is helical. And a long end to end distance constrains the peptide to be straight, hence largely limiting the conformational space available to the unfolded peptide.

In that respect your test case might not be a great one, as alanine is known to show a strong bias towards helical conformations. Hence in that particular case the helical structure will be dominant for shorter distances whereas this might not be the case for your peptide. I would think about trying some other CV that would describe the end states of interest better (such as H-bonds and dihedral angles or the AlphaRMSD variable available in PLUMED).

How long were your simulations? A 24 residue peptide has a much more conformational freedom than a 10 residue peptide, especially when unfolded. So much larger variations in the calculated free energy should be expected due to sampling issues.



Dr. Niklaus Johner
University of Basel
Klingelbergstrasse 50 / 70
CH - 4056 Basel
Tl: 076 302 12 20

On 28 Jan 2015, at 00:09, MEHRAN MB <> wrote:

> Dear NAMD experts,
> I am trying to compare free energy of forming helix structure for two coils with 28 residues in length. Both are identical except, in one all GLU are substituded by ALA. Indeed, I want to measure these residue contribution in forming helix, and I need to calculate Free energy with high precision.
> I tried ABF method and it works great for deca-alanine in vacuum. I run multiple simulations and all gave me pretty consistence results, both in curve shape and final value. free-energy vs reaction-coordinates result is provided. (Also when I solvate them in water I could not get good result)
> <deca-alanine_vacuum.png>
> However trying ABF on my 28 res polypeptide in vacuum, set boundary on end-to-end distance to vary from 40A to 80A and #samples within 40000 to 200,000; I have seen pretty inconsistency in free energy curve and final value. Since there are few charged residues I thought it might trapped in a non-equilibrium state.
> I divided the ABF process to smaller windows. I tried first small window, end-to-end distance varying from 40A to 45A and sampling from 100,000 to 200,000, and I am still getting pretty inconsistent result ( from 5 to 10 Kcal/mol ) for this window.
> So I believe I have enough sampling but it does not necessary mean that It has been sampled in equilibrium state. So How I can make sure that I am sampling in quasi-equilibrium process ?
> Next step would be measuring this helix unfolding Free energy in solution since I doubt I can say anything about the free energy in solution from vacuum simulation results. (I might be wrong, )
> any advice help to improve ABF results or suggestion about other methods will be appreciated,
> Best,
> Mehran
> UOttawa
> here is simulation details:
> 0.5 timesteps
> rigidbond none
> 0.1 bin width
> 1000 fullsampling

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