AMBER Archive (2008)

Subject: Re: AMBER: Discontinuous Constant pH Restarts

From: Smriti Sharma (ssmriti_at_gmail.com)
Date: Thu May 08 2008 - 06:05:31 CDT

Dear Amber Users,

I too have noticed, similar discontinuity in my restart files as reported by
Neil. As suggested by Dac in his previous mails, i tried to run short
simulations as well as i tried to run parallel and serial jobs (as Neil
suggested). Still that discontinuity is observed, i.e., running in serial as
well as in parallel doesn't affect the results obtained.

I am using Amber9 on fedora8 with gfortran as compiler for constant pH
simulation.

Regards

Smriti Sharma

On Thu, May 8, 2008 at 3:04 AM, David A. Case <case_at_scripps.edu> wrote:

> On Wed, May 07, 2008, Neil Bruce wrote:
> >
> > I've since tried a few tests and found that this problem only occurs
> > when executing Sander in parallel, the serial code restarts as expected.
> >
> > I've run tests on three computers and found the same behaviour (one
> > Linux/x86_64/ifort 9/mpich2, one Linux/ia64/ifort 9/bullmpi and
> > another that I don't have the details of at the moment but can get if
> > it helps). On the two computers I've given details for, the cnstph
> > test runs without error. 'Standard' GB simulations also restart
> > properly.
> >
> > Could this be a compilation error?
>
> Looks/tastes/sounds like a bug to me. I've entered this into bugzilla, and
> we
> will try to see if we can figure out what is happening. (Maybe something
> in
> the cpin file is not being correctly broadcast to all nodes...; or
> something
> along those lines.)
>
> Thanks for the report....dac
>
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