From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Aug 23 2016 - 20:29:37 CDT
Hi JC, what you describe for RMSD is the result of the Jacobian term of the
collective variable definition (handled explicitly by thermodynamic
integration and ABF, implicitly by others). In the case of RMSD, the term
can be quite significant and it yields a logarithmically diverging free
energy profile at RMSD ~ 0.
For eigenvector, there is also a Jacobian term that depends on the
anisotropy of the various eigenvector components. See the Appendix of
Jérôme's and my Mol Phys paper for the expressions of the two terms.
I definitely don't think that the two endpoints are more accurately
represented than any other.
Aside from those considerations (which could be difficult to use in
practice), have you considered setting the fitting/reference structure in
between the two endpoints, so that the transformation goes from -1 to +1?
On Tue, Aug 23, 2016 at 9:02 PM, JC Gumbart <gumbart_at_physics.gatech.edu>
> Hi all,
> I used the eigenvector colvar for a simple transition between two close
> states of a protein (RMSD = ~2.6 A). One curious thing I observed is that
> the minimum falls at 0.5; in fact, I saw this in other runs as well, even
> using different starting structures. For something like RMSD, it seems
> obvious that there will be more conformations accessible the more you
> increase RMSD, which would lower the energy. I can’t convince myself if
> that is the case here, however. Certainly, it seems that each value of the
> colvar (in my case normalized from 0->1) does not dictate a unique
> structure, but is there a clear relationship with where one is on the path
> and the number of accessible states? In which case, only the end points
> can truly be trusted?
-- Giacomo Fiorin Associate 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 Scholar: http://goo.gl/Q3TBQU Personal: http://giacomofiorin.github.io/ Lab page: https://icms.cst.temple.edu/members.html *"As computer programmers we have a responsibility to make sure that we run the computers instead of the computers running us."* - Steve Oualline
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