AMBER Archive (2003)

Subject: AMBER: EWALD BOMB and solvent density problem

From: northrop_at_chem.ucla.edu
Date: Thu Sep 11 2003 - 13:28:51 CDT

I'm running a MD simulation of a [2]Rotaxane and trying to use an acetonitrile solvent model.
My protocol is 1) 1000 steepest descent minimization 2) warming up from 0 K to 300 K with a
constant volume run of 100 ps 3) a productive run at 300 K of 500 ps at constant pressure. I'm
using AMBER7, the default vlimit of 20, and bugfix.38 has been applied, however, after around
30-50 ps but I get 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." I've
looked at the resulting restart file and noticed large voids in the solvent. I believe this may be
the result of the incorrect solvent density from my .crd and .top files. When I use solavteOct in
LEAP to add the acetonitrile solvent, the acetonitrile solvent molecules are arranged in an
extremely regular, unequilibrated grid pattern instead of an equilibrated pattern with the right
density. Is it possible to define the solvent density in LEAP? Is there a way to create a pre-
equilibrated box of the acetonitrile solvent so I that the density is correct when I solvate in LEAP
(I know that these exist for the solvents already included with AMBER7 in amber7/dat/leap/lib)?
The parameters I'm using for acetonitrile are those from the six-site model of Jaime et. al. (JOC,
21, 10, 901- 908). Any help would be greatly appreciated.

Thanks in advance,
Brian Northrop

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