AMBER Archive (2004)

Subject: Re: AMBER: getting new box info

From: Melinda Layten (mlayten_at_gmail.com)
Date: Thu Oct 28 2004 - 10:46:57 CDT

I had a similar problem with simulations when water molecules had
traveled many periodic boxes away from the starting point. By adding
iwrap=1 (which images all molecules back to the starting box
periodically) everything worked nicely again.

Good luck

Melinda Layten

On Thu, 28 Oct 2004 07:39:07 -0700, David A. Case <case_at_scripps.edu> wrote:
> On Thu, Oct 28, 2004, Vincent Bisetty wrote:
>
>
> > I am experiencing problems with the restart of the MD simulation
> > It seems like the box info is not being read?
> >
> > Here is the input file:
> >
> > equilibration at 300 K using PME
> > "out16900a17000ps.out" 47 lines, 2772 characters <== is this really in
> the output file?
> > /
> > &ewald
> > skinnb = 1.0,
> > /
> >
> >
> >
> > --------------------------------------------------------------------------------
> > 1. RESOURCE USE:
> > --------------------------------------------------------------------------------
> >
> > | Flags: SGIFFT MPI
> > getting new box info from bottom of inpcrd <== this is a normal line
> it does not indicate
> a problem
>
> >
>
> You error may be something different than you think. The line about getting
> box information is expected (you should see that in all of your simulations,
> I think).
>
> More investigation will probably be necessary to figure out what is happening.
>
> ...good luck...dac
>
>
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