AMBER Archive (2005)

Subject: Re: AMBER: need clarification on EWALD BOMB error

From: Thomas Cheatham (cheatham_at_chpc.utah.edu)
Date: Thu Nov 17 2005 - 11:45:28 CST

> i am doing 1ns dynamics for some set of protein molecules whose AA sequence
> varies at only one position. i did dynamics for 7 molecules and got the
> results successfully by same procedure. when i repeat the same procedure for
> 8th molecule it produces EWALD BOMP error in equilibration process. i
> searched the previous quires in the amber reflector sites it say i have to
> change the conditions slightly like in the following amber page
> http://structbio.vanderbilt.edu/archives/amber-archive/2002/1120.php
> i don't know, is it advisable to change the parameter for one calculation.
> how much this parameter will affect the dynamics. please give some good
> suggestion on this problem. i attached my output files also here for
> equilibration process

As suggested in that e-mail in the archive, and in the output file...

  EWALD BOMB in subroutine ewald_list
    volume of ucell too big!!
   a regular restart should fix things

A restrt should continue, but likely there is something causing the box
to expand relatively quickly. Note that you have a very long and thin
box; as the rotational correlation times of these molecules is relatively
rapid, you could run into issues later where rotation of the protein
causes it to interact with its periodic images.

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
-/-
/-\ tec3_at_utah.edu (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A http://www.chpc.utah.edu/~cheatham

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