Adrian -
Well, actually there are lots of users out there who probably started using
amber before Ross' excellent tutorials were available. I have looked at
some, but not all of the tutorials, and I have nothing but praise. I don't
recollect what they say about ntwx settings, and have not plowed through
them all to see. One problem with tutorials though, is typically they are
trying to show how to use features with a toy problem so the user can
produce results in a reasonable time. SO it would be understandable if a
tutorial generated a short trajectory using higher frequency snapshots.
Maybe the tutorials do cover this, but as I say, I am sure not everyone has
been through every page. Okay, back to the manual. I perused it quickly.
It has at least two early examples with ntwx set to 100. It has one example
with it set to some huge number, rather than just not setting it or setting
it to 0 (so this can produce confusion). It has a couple of examples of it
set to 500 for PB (that is too high a frequency unless dt = .002 - I don't
remember what it was). It has one charming example of a MINIMIZATION being
run with ntwx and a few other things that make no sense being set to
moderate numbers. I am a details freak, and I spot inconsistencies pretty
readily. Other people copy inconsistencies rather readily. If you go out
on the amber mail reflector archive and search for ntwx, you will find 100's
of instances of ntwx being set to 50, 100, - small numbers that apparently
don't make sense for most purposes. The more that we strive to make our
stuff work well for our users, the more they will appreciate us, reference
us in their publications, and keep coming back for more.
Best Regards - Bob
----- Original Message -----
From: "Adrian E. Roitberg" <roitberg.qtp.ufl.edu>
To: <amber-developers.scripps.edu>
Sent: Friday, May 05, 2006 9:58 AM
Subject: Re: amber-developers: Troubles at PSC
> Robert and list:
> As for the guidelines, I always thought that you give the user enough rope
> to
> hang themselves with ;-) However, by reading the examples in the manual,
> the test cases, and
> the tutorials, the user should get a good idea of what types of 'flags' to
> use.
> Basically, the tutorials from Ross use reasonable time steps, etc.
> if the user wants to try running amber without looking at those, adding
> text into the manual warning them will not quite help either.
> Cheers
> Adrian Roitberg
>
Received on Sun May 07 2006 - 06:07:06 PDT
