Re: (No subject)

From: Richard Wood (
Date: Mon Jul 10 2006 - 19:58:12 CDT

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 L. Wood, Ph. D.
Computational Chemist
Cockeysville, MD 21030

----- Original Message ----
From: Mark Abraham <>
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.


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