From: David A. Case <>
Date: Thu, 25 Sep 2003 13:25:23 -0700

On Thu, Sep 25, 2003, wrote:

> Amber users - I'd like to run some simulations in an acetonitrile solvent
> but I don't know how to make a pre-equilibrated solvent box similar to those
> that exist for CHCl3, water, etc. The parameters I'm using for acetonitrile
> are those from the six-site model of Jaime et. al. (JOC, 21, 10, 901- 908).
> My procedure for trying to equilibrate a box of acetonitriile is as follows:
> in leap, I set the restype of MeCN to solvent and then solvate a 10 box on
> MeCN 1000 step steepest descent minimization 20 ps constant volume run to
> raise the temp to 300 k 200 ps constant pressure run to equilibrate
> Unfortunately the program always fails with the error message "EWALD BOMB in
> subroutine, ewald_list, volume of ucell too big, too many subcells, list
> grid memory needs to be reallocated, restart sander." When I look at the
> restart file, there are large voids of no solvent within the periodic
> boundary. Any help anyone could give me about how to make a
> pre-equilibrated MeCNBOX would be greatly appreciated.

Does the program fail in the constant pressure part? What value of taup are
you using? If it is less than 5 ps or so, you might try making that larger.
Otherwise, post the input files of something that fails, and Mike will get it
fixed right away :-)


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 Sep 25 2003 - 21:53:01 PDT
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