From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Wed Dec 08 2010 - 11:09:53 CST
Ajasja,
Some partial answers, if you restrain the whole backbone still you can
"unlock" two backbone atoms that want to be included in ABF
calculations. Try some short run of whole system (few ns) to see how
lipid tails are really relaxed without applied force, than decide. Think
that ~ 750 samples will be OK. 4th question is not 100% clear, but if
you have a well prepared MD run, using ABF or not, sidechains cannot
overlap the backbone. See J. Chem. Theory Comput. 2010, 6, 35–47 for
some examples of BAF usage, also J. Chem. Theory Comput.
10.1021/ct100413b could be useful.
Branko
On 12/8/2010 5:31 PM, Ajasja Ljubetič wrote:
> Dear all,
>
> I would like to explore the conformational space (ie the free energy
> landscape) of the side-chain of a spin label (MTSSL
> <http://www.meilerlab.org/web/images/research/epr2.jpg>) in water and
> in the membrane. The side chain has five dihedral angles (chi1 to
> chi5). I'm thinking of using ABF for this purpose, but the following
> questions arise:
>
> * What would be a sensible value for the fullSamples value? (Since
> lipid tails may relax slowly, probably something in the range of
> 500-1000).
> * The first dihedral angle is composed of two backbone atoms. If I
> restrain the backbone, does the first chi angle still count
> as unconstrained (does it fulfill the requirements for a well
> defined ABF colvar)?
> * Would metadynamics be a better choice? What would be a good
> hillHeight? (about 1/tenth of the highest torsional energy barrier).
>
>
> And some more phylosophical ones:
>
> * What happens in the conformations where the side chain overlaps
> the backbone? The free energy there is really high due to VDW
> contacts. Does ABF push the sidechain through the backbone?
> * Is it even feasible to explore a 5D space using ABF? I'm
> thinking of using a bin width of either 15 or 30 degrees (~250k
> or 8M bins).
>
>
> I would love to hear some feedback from people who have
> some experience using ABF.
>
> Best regards,
> Ajasja Ljubetič,
> Young researcher,
> Department of solid state physics (F5),
> Institute Jožef Štefan,
> Ljubljana, Slovenia
>
>
>
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