amber-developers: citation

From: Yong Duan <>
Date: Sun, 28 Jan 2007 21:30:35 -0800

Following the line of discussion on citations, I think we need to look into
the citation issues of the force fields too. In my opinion, ff citation is
actually even messier. We need to come up with a "standard" set of citations
and may recommend citations of multiple papers when a particular flavor of
ff is used.

For example, I'd think a sensible set of citations of ff99 and ff96 should
also include the ff94 paper. Similarly, ff03 and ff02 citations should
include the ff99 paper because most torsion parameters were actually
"borrowed" from the ff99 paper. If we do not use this "multi citation" set,
we give users the wrong impression that the improved ff is a "new" one
(which is, of course, partially true). The multi-paper citation also
encourages the users to understand the progression and the genealogy of the

If we establish reasonable rules, we attribute the credit appropriately and
everybody will be happy. This can encourage further development and reduce
the level of confusion. Regardless how careful or how deligent we are at the
development stage, further improvements will likely be needed because, as we
gather more data and experience, it will be inevitable to adjust a few
parameters to improve some aspects of the force field. Keep in mind,
computer power doubles every 1.5 years (about 100 times every 10 years). So,
whatever the test we do now will be considered somewhat "too little" 10
years later simply because more can be done a lot more easily. A result of
this is that we may need to update some of the parameters. Hopefully, if the
force field is designed well, we only need to change a few parameters.

Please let me know your opinion, particularly those involved in ff

Received on Wed Jan 31 2007 - 06:07:17 PST
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