From: hurst@hyper.hyper.com (Graham Hurst)
Subject: Re: Publishability of Mechanics Calculations
Summary: All details should be published.
Reply-To: hurst@hyper.com (Graham Hurst,,)
Organization: HyperCube Inc.
Date: Tue, 15 Sep 1992 17:53:36 GMT

In article <1992Sep10.112507.6659@cc.ic.ac.uk> rzepa@ic.ac.uk (Henry Rzepa) writes:
>Prof Kenny Merz (merz@retina.chem.psu.edu)
>is soliciting opinions about whether molecular mechanics calculations
>which have used non-published parameters (in house, proprietary,
>developmental
>etc) can be quoted in scientific journals. 
>
>Does anyone have any opinions?
>_____________________________________________
>|  Dr Henry S Rzepa.                       Tel:   +44  71 225 8339 
>|  Department of Chemistry           Fax:   +44 71 589 3869  
>|  Imperial College                        Email: rzepa@ic.ac.uk
>|  LONDON SW7 2AY
>| Sent using Eudora 1.3b46.                 
>_____________________________________________


Only in the Journal of Nonreproducible Results!

<Climb on to soapbox>

It is a foundation of science that results only be published if enough
information is given to allow independent confirmation of the results.

In ab initio quantum chemistry it is a hard and fast rule that a paper
will be turned down if the basis set is not completely disclosed or
referenced, and I was appalled when I discovered that the same standards
are not always applied to molecular mechanics!

Unfortunately referees and editors have allowed some molecular mechanics
results to be published without full disclosure of the functional
form or parameters.  While in many cases there have been minor omissions
that the authors are happy to disclose when asked, I have heard three
defences for purposely publishing results based on unpublished parameters:

1. Finger pointing: "X hasn't published parameters either" or "I got the
   parameters from Y, (s)he should publish them".  I don't accept either
   flavour of this buck passing - either you take responsibility for your
   results or you don't publish.

2. "There are too many numbers to be included in a manuscript." Many
   journals now have microfilm supplements for things like large tables
   of numbers, and parameters could also be put in the public domain
   by depositing at ftp sites.  (There was talk a few years back about
   establishing a parameter repository at the NBS, but I don't think
   anything came of it.)

3. "You can reproduce my results if you use the same program." This is
   *not* independent reproduction! That is akin to saying "if you buy
   the same NMR spectrometer as I did you can reproduce my NMR results,
   but you won't be able to if you buy someone else's or build you own"!
   If nothing else, the results may be tainted by program errors. 

It's my opinion that one shouldn't quote results from molecular
mechanics calculations which have used non-published parameters
in scientific journals.  If the parameters are developmental don't
quote results until you have enough confidence in the parameters
to publish them.  If the parameters are in-house or proprietary,
the results should be as well.

I only wish more referees considered reproducibilty when deciding to
accept papers with molecular mechanics results.  I have personally
tried to reproduce such results after reading papers describing the
force fields, and in almost all cases this could not be done without extra
information from the authors.  It was particularly disturbing to find
a force field author who would not divulge parameters and acknowledged
that a long list of that author's publications were thus not
reproducible!

<Climb off of soapbox>

Graham
Newsgroups: sci.chem