AMBER Archive (2003)

Subject: Re: AMBER: Ewald problem

From: Shuang Ding (sd517_at_nyu.edu)
Date: Wed Jul 30 2003 - 12:28:31 CDT

Thanks for your reply.
What's bugfix.38 for?
I use Amber7, and the system was heat up at constant volume. The equilibration protocol is: (1)5000 steps of steepest minimization with 10kcal/mol constrain on 11mer DNA; (2) 30ps MD at 10k keeping the constrain; (3) warm up from 10k to 300k for 60ps MD at constant volume and continue 20ps at 300k, also 10kcal/mol constrain on DNA; (4) 30ps MD at 300k at constant pressure, constrain decrease to 1.0kcal/mol; (5) 30ps MD at constrain 0.1kcal/mol.

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Wednesday, July 30, 2003 1:01 pm
Subject: Re: AMBER: Ewald problem

> 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
>
> --
>
> ==================================================================
> 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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