From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Jan 28 2015 - 14:52:54 CST
There is no universally defined reaction coordinate for the unfolding of an
alpha-helix.
FYI in one of the first applications of the colvars module (Henin et al,
JCTC 2009) we used three variables to really nail deca alanine in vacuo.
On Wed, Jan 28, 2015 at 3:50 PM, MEHRAN MB <mb.mehran1_at_gmail.com> wrote:
> Thank you so much for you quick reply,
>
> Niklaus, I totally agreed that shorter end to end distance does not
> necessary mean that the peptide is helica. Dihedral angles as a CV, only
> have four groups of atoms available regarding one single torsion angle,
> which means, I guess, 56 torsion angles need to be defined to cover all phi
> and psi dihedrals in 28 peptide chain?!?! Also I am not sure what should I
> considered as a reaction coordinates ? it is the same with h-bond colvar,
> there are many reaction coordinates correlated together!! I have no
> experience with this Colvar, so sorry if it is a naive question.
>
> ps: I ran 50ns for 5A windows (40 - 45) still not getting results
>
> Ajasja, I have not read that and I took a quick look, it should be a great
> starting point to see if I can resolve my issue. Hopefully there are some
> NAMD friendly solution in this paper.
>
>
> Thank you again, and I will keep you posted if I find any solutions.
>
>
> Best,
> Mehran
>
> On Wed, Jan 28, 2015 at 5:05 AM, Ajasja Ljubetič <
> ajasja.ljubetic_at_gmail.com> wrote:
>
>> 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
>>>
>>>
>>>
>>
>
-- Giacomo Fiorin Assistant Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 https://icms.cst.temple.edu/members.html http://giacomofiorin.github.io/
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