Re: [AMBER] Query- Heating after Equilibration

From: Jason Swails <>
Date: Sun, 20 Jun 2010 11:47:04 -0400

On Sun, Jun 20, 2010 at 11:32 AM, case <> wrote:

> On Sun, Jun 20, 2010, Jagdeesh C wrote:
> >
> > I am trying to perform a few ps heating. I have the prmtop,, and
> > restart file which seem to look fine. However the heating simulation
> doesn't
> > work and the final files are not generated (no output). I have been
> trying
> > to rectify it but I seem to be going wrong somewhere. Can someone please
> > help me and let me where I might be going wrong?
> >
> > Many thanks,
> > Jagdeesh
> >
> >
> > ./sander.MPI -O -i -o heat_143d.out -p 143d_sol.prmtop -c
> > min_143d.rst -r heat_143d.rst -x heat_143d.mdcrd -ref min_143d.rst

Professor Case is right -- mpirun or mpiexec or something of the like (it
differs based on the system) is typically needed to run sander.MPI, though
this usage usually starts a single sander.MPI thread on my machines (i.e. it
will be more or less the same as running serial sander). This may not be
true for all MPIs, though, I don't know.

However, why are you using "./sander.MPI"? Is sander.MPI in the directory
you're trying to run from? That seems like an unusual choice, since
sander.MPI is usually in $AMBERHOME/bin, and I'd suggest that running jobs
in that directory should be avoided (though it won't cause any errors).
(Unless of course you're creating a link in your current directory to
$AMBERHOME/bin/sander.MPI) Do you get any complaints from the command line,
such as not being able to find sander.MPI?

All the best,

> You need to use mpirun with sander.MPI: you can't just call it directly.
> I'm not sure if this is the reason you are getting "no output", but it's
> certainly worth checking.
> General advice: if you are having problems, run the serial version of the
> program, use just a few steps (say 50, not 50,000), set ntpr=1, and very
> carefully study your output files. Later on you can increase the number of
> steps, etc.
> ...good luck...dac
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Sun Jun 20 2010 - 09:00:04 PDT
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