AMBER Archive (2003)

Subject: Re: AMBER: Ewald problem

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 30 2003 - 12:01:49 CDT

On Wed, Jul 30, 2003, Shuang Ding wrote:
>
> I'm running a MD simulation of damaged DNA with base adduct. The system got
> blow up at about 600ps with error message "SHAKE cannot be accomplished".
> Then I try to restart the MD before the blowup and reassign velocities, the
> production stopped at around 100ps with error "EWALD BOMB in subroutine
> ewald_list, volume of ucell too big, too many subcells, list grid memory
> needs to be reallocated, restart sander".

a. be sure you have applied bugfix.38 from the Amber web site

b. be sure you have equilibrfated to 300K at constant volume before moving
   to constant pressure

c. be sure you are using vlimit: it's on by default in amber7, but it's not
   clear which version you are using.

..good luck..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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