AMBER Archive (2002)

Subject: Re: Gibbs tutorial problem

From: David A. Case (case_at_scripps.edu)
Date: Thu Jul 25 2002 - 14:03:17 CDT

On Thu, Jul 25, 2002, yuann wrote:

> When I follow all steps in Gibbs toturial(Valine to Alanine Free Energy
> determination), the final md before gibbs run seems bad, ie. WAT diffuse
> and it can't continue Gibbs run.
>
> (If I use this coordinate, Gibbs return warnning message as follow)
> WARNING: Atom # 376 more than 1 box length from the central box image.
> WARNING: Atom # 626 more than 1 box length from the central box image.
> WARNING: Atom # 812 more than 1 box length from the central box image.
> WARNING: Atom # 1006 more than 1 box length from the central box image.
>
> I use AMBER6, all force field files, leap source files, input script files
> are the same as this toturial describes. However, I still have no idea
> what mistake I made.

This looks to me like an error in the tutorial...:-( The simplest fix is to
add "iwrap=1" to the &cntrl namelist in the sander equilibration. This
*should* keep everything near the central box, (which is what gibbs requires).

I've asked the tutorial author to look into this; we'll also try to get some
more detailed outputs incorporated into the tutorial. But give this
suggestion a try for now. (It's also possible that something else went wrong
with your equilibration, so check that out as well.)

Thanks for pointing this out....dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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