From: <>
Date: Thu, 25 Sep 2003 19:35:03 -0000

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.

thanks in advance,
Brian Northrop

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Sep 25 2003 - 20:53:01 PDT
Custom Search