Re: (No subject)

From: JC Gumbart (
Date: Mon Jul 10 2006 - 20:11:31 CDT

We should all try to be kind to our fellow users on this list but at
the same time, not be overly sensitive to what we read. Meaning and
attitude both are often lost in translation here. As such, we
shouldn't try to read too much into what was in fact a helpful reply.

And instead of attacking what we perceive to be deficiencies in a
certain response, make up for them! Post the relevant link: (there is a lot of good
information here and I'm sure many people often overlook it)

 From now on, keep this list for science and software discussions
only please, lest we devolve into nearly every other forum on the

On Jul 10, 2006, at 7:58 PM, Richard Wood wrote:

> In defense of the original poster, perhaps he has tried the
> tutorials. Maybe his system similar to that of the tutorials so
> he's used (default or) similar cutoffs.
> Or maybe he doesn't know how to find them and you could send them
> (or links to them) to him?
> Not everyone in the world of computational chemistry is lazy, we
> just try to maximize the amount of productivity in amount of time
> that is available to us to do computational work.
> Richard
> Richard L. Wood, Ph. D.
> Computational Chemist
> Cockeysville, MD 21030
> ----- Original Message ----
> From: Mark Abraham <>
> To:
> Sent: Monday, July 10, 2006 7:52:23 PM
> Subject: Re: namd-l: (No subject)
> >
> > After the minimization, the protein (in a water box) looks
> terrible in
> > VMD! And in the log file it
> > keeps saying "Warning: Bad global exclusion count, possible error!
> > Warning: Increasing cutoff during minimization may avoid this.".
> > Is the small cutoff value responsible for such a poor
> representation or
> > can I do something else to
> > change it?
> Yes, probably. Please give some details about what you're doing -
> like the
> size of your cutoffs... If you're new to this, please try some of the
> tutorial exercises available on the NAMD website.
> Mark

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