Re: a bug? Re: AMBER: one more line about the npscal, box size changes and rms

From: David A. Case <>
Date: Thu, 7 Aug 2003 11:35:46 -0700

On Thu, Aug 07, 2003, Haizhen Zhong wrote:
> According to my understanding from these two reply, it seems it's better to
> use npscal=1 rather than npscal=0. Since npscal = 0 is default value, there
> may be some reason to use npscal=0 in certain cases and in other cases, it
> may be better to use npscal=1. Now my new question is:
> "Are there some rules that define when is it best to use npscal=0 and when
> to use npscal=1? Is there any guideline in the manual?"
> Or according to Yong's indication, is there a bug when npscal is set to 0?
> In such case, does it mean not to use npscal = 0 at all?

My personal (maybe idiosyncratic) view: the problem is with ibelly=1, not
really with npscal. I don't see any reason why anyone should ever use the
ibelly option; if you want to prevent the protein from moving (much) during
equilibration, use ntr=1 instead.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Thu Aug 07 2003 - 19:53:01 PDT
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