From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Jan 28 2015 - 04:05:37 CST
Exactly, choosing the colvar(s) is crucial. Meheran, have you perhaps
read Comer
et. al <http://pubs.acs.org/doi/full/10.1021/jp506633n> [1], in particular
the section "Hidden Barriers and Other Challenges to Obtaining Accurate
Results"?
Best regards,
Ajasja
1.
Comer, J. *et al.* The Adaptive Biasing Force Method: Everything You Always
Wanted To Know but Were Afraid To Ask. *J. Phys. Chem. B* (2014).
doi:10.1021/jp506633n
On 28 January 2015 at 10:49, gmail <niki.johner_at_gmail.com> wrote:
> Hi,
>
> 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.
>
> Best,
>
> Niklaus
>
> Dr. Niklaus Johner
> University of Basel
> Klingelbergstrasse 50 / 70
> CH - 4056 Basel
> Tél: 076 302 12 20
>
>
> On 28 Jan 2015, at 00:09, MEHRAN MB <mb.mehran1_at_gmail.com> 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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