Using ABF to explore the conformational space of a spin label attached to a membrane protein

From: Ajasja Ljubetič (
Date: Wed Dec 08 2010 - 10:31:16 CST

Dear all,

I would like to explore the conformational space (ie the free energy
landscape) of the side-chain of a spin label
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
   - 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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