AMBER Archive (2003)

Subject: Re: AMBER: vlimit?

From: David A. Case (case_at_scripps.edu)
Date: Mon Dec 22 2003 - 11:24:18 CST

On Sun, Dec 21, 2003, Ran Ye wrote:
>
> I'm basically following the steps on the "DNA"
> tutorial
> to do some MD on proteins. I couldn't get my dynamics
> going because "vlimit exceeded" and "Coordinate
> resetting (SHAKE) cannot be accomplished". Does anyone
> know how to fix it?

In addition to what Bill Ross suggested, don't try a constant pressure
simulation until you have reached a good temperature at constant volume,
turn down the size of the restraints (from 500 to about 5), and use a
larger value of taup (say 2-5) when you _do_ use constant pressure.

..hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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            |    http://www.scripps.edu/case
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