R: RE: R: RE: R: RE: R: RE: R: RE: R: Re: R:[gmx-users] Tabulated potential - Problem

Berk Hess gmx3 at hotmail.com
Thu Oct 1 22:51:46 CEST 2009

> Date: Fri, 2 Oct 2009 06:10:37 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: R: RE: R: RE: R: RE: R: RE: R: RE: R: Re: R:[gmx-users]	Tabulated	potential	- Problem
> Berk Hess wrote:
> > Ah, I thought the sentence in one of my previous mails was clear enough:
> > "The points in the table_b.xvg file should be equally spaced.
> > grompp assumes equal spacing, but does not check this."
> > 
> > I think "should be" and "must be" are equivalent in this context.
> > But we can clarify the manual, and add a check in grompp.
> It's close, but in general there is a shade of certainty conveyed by 
> "must" that is additional to that of "should". The dictionary I have to 
> hand contrasts "to be obliged or compelled to, as by some constraining 
> force or necessity" with "to denote duty, propriety, expediency" 
> respectively. Wiktionary agrees - http://en.wiktionary.org/wiki/must. I 
> am aware of usage in a body of law where failure to follow a direction 
> qualified by "must" carries a more severe consequence than failure to 
> follow a direction qualified by "should".
> Berk is correct in this context, however. The only relevant qualities of 
> the table are that it be accurate and reasonably efficient. A user 
> failing to follow "should" would be making an unwarranted assumption 
> that accuracy and/or efficiency was compromised only to a negligible 
> degree. "must" is slightly superior in such a context where no purpose 
> is served by the distinction with "should," and the reader might err 
> more often when "should" is used. Manual section 6.7.1 certainly 
> expresses the idea that equal spacing of table points is normal and 
> expected, but there is no statement which conveys a suitable degree of 
> definiteness. That could be improved.

I am aware of these subtle differences.
I am not a native English speaker (although I did live in Australia
for 3.5 years during my childhood). But I personally do not like
a manual description which repeatedly uses the word "must",
it just doesn't sound very friendly. I strongly prefer "should".
But we could also use something like "has to have".
Anyhow, I'll put a check in grompp, so the user will get a fatal error
and can not proceed, even if he/se interprets the manual differently
from intended. Such a check doesn't have any disadvantages (except
for requiring 5 minutes of coding and checking) and also help to detect
mistakes in script generating tables etc.
This is becoming more important, as more and more people start using
numerically derived potentials.


> Even the use of language can be as exacting as the methods described by 
> it :-) I tied myself in knots last weekend with an incorrect use of 
> "abjure" instead of "adjure"...
> Mark

What can you do with the new Windows Live? Find out
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091001/76b48af1/attachment.html>

More information about the gromacs.org_gmx-users mailing list