On 9/12/13 7:04 PM, Rafael I. Silverman y de la Vega wrote:
I see,
when you say thorough parametrization and validation, what do you mean?
How does one validate the system, calculate free energy in solution and
compare it to tabulated data?
The target data depend on the force field for which parameters are being
developed. Matching QM geometries, water interaction energies and distances,
free energies of solvation, crystal structures, liquid properties, etc. are all
useful depending on the underlying force field and how it was derived. For
bonded parameters, matching QM energy scans and/or vibrational properties are
common.
-Justin
On Wed, Sep 11, 2013 at 4:57 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 9/11/13 6:07 PM, Rafael I. Silverman y de la Vega wrote:
Hi all,
in another thread it was recommended that instead of changing the atom
types by analogy to ones with the desired parameter already assigned, that
instead one should assign bonded parameters by analogy. I was just
wondering how this is better?
I didn't suggest that. I said that any assignment by analogy can have
negative outcomes. Bonds and angles, in theory, are a bit easier to deal
with because the nonbonded interactions between their atoms are excluded.
Torsions are very difficult because the torsional bonded terms have to be
balanced against the charge and LJ parameters of atoms separated by 3
bonds, i.e. 1-4 interactions.
Let me state very clearly that, for any missing parameters, anything short
of a thorough parametrization and validation is (in my purist mind) unsound.
As long as the atom type isnt too different, then why would the torsions
not work out right? If the parameters are interrelated, what makes it
better to add one term to an atom type rather than changing all the terms
(to ones that are supposed to be together)?
The key is being sufficiently similar, but even subtle differences between
LJ parameters have very large consequences, especially for 1-4
interactions, so I find it hard to believe that one will recapitulate
accurate interactions in this case. Of course, all assignments by analogy
bear some penalty for nonequivalent groups. I balked at your initial post
in the other thread because there was no need to mess with atom types. The
system at hand there contained protein and lipid and could be completely
described by existing atom types and bonded types, the OP there was just
(and perhaps still is) constructing the force field incorrectly. I felt it
need to be stated that the approach there would not necessarily be
productive, and to make sure the archive was complete so that no one would
come across a post in vacuum and assume that he or she can simply swap
around atom types to make error messages go away. Your initial statement
referred only to bonds and angles, which indeed would be insensitive to
changes in LJ parameters on any of those atoms, but since the thread was in
the context of dihedrals, I thought I should state my opinion there.
-Justin
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Justin A. Lemkul, Ph.D.
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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