[gmx-users] Gel Phase in DMPC using Berger force field ?? -- Focus: naming convention
chris.neale at utoronto.ca
chris.neale at utoronto.ca
Wed Dec 12 19:19:48 CET 2007
> Several points:
> What is called the Berger force field was
> actually developed by See-Wing Chiu in our lab
> and presented in a 1995 paper. The Berger et al
> paper tested this force field against another
> candidate and found that it was better, and that
> is the paper that has been cited ever since.
I agree that it is incorrect to refer to this as the Berger
forcefield, although I have myself referred to it in this way for
informal discussions. If one were to discuss the important
contributions I would refer to the following papers
(Jorgensen_1988/Egberts_1994/Chiu_1995/Chiu_1996/Berger_1997), and of
course the Ryckaert-Bellemans contribution is also important.
Perhaps I have missed some, but in that case it is not intentional.
I would be interested to participate in a discussion about the naming
convention for these parameters. For example, it is unclear to me why
one would refer to them as the 'Chiu parameters' as opposed to the
'Egbert parameters', or even the 'Ryckaert-Bellemans lipid
parameters'. I would also accept an acronym from the first authors
such as RBJECB. For detailed methods sections I am in the habit of
referring to it by a chronological sentence as opposed to by a short
name, but for informal discussion a short name is certainly convenient.
To be clear, I am not arguing against calling then the 'Chiu
parameters' but would be in favour of more discussions on the topic.
> See-Wing did tests of the necessary VDW cut-off
> for accuracy against what seemed like the most
> sensitive test, the value of the dipole potential
> at the water-lipid interface, and concluded that
> one should use a cut-off of at least 18 angstroms.
> The van der Waals parameters for the hydrocarbon
> tails were reparameterized in a paper we
> published a few years ago, and in that paper we
> verified that the 18 angstrom cutoff was required
> for an accurate liquid hydrocarbon simulation also.
> Recently See-Wing has reparameterized the van der
> Waals parameters in the lipid head groups, using
> specific volumes of liquids comprised of small
> molecules that are part of the head group. The
> resulting force fields, which retain the partial
> charges of the Berger-Chiu field, work very well
> in replicating x-ray structure factors of lipids
> with various chain compositions, but he has not
> yet tried to do gel phase--that would be
> interesting. The journal ms. is still sitting on
> my desk, I am afraid, but there is a pretty good
> description of the parameterization in a chapter
> in a book that Scott Feller is editing, which we
> can send on request, as well as the lipid
> complete force field in itself. We believe it is
> state of the art at this time.
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