AMBER Archive (2003)

Subject: Re: AMBER: mpi in mm-pbsa

From: Shuang Ding (sd517_at_nyu.edu)
Date: Thu Aug 07 2003 - 15:14:53 CDT

It works now, thank you very much Dr. Holger.

----- Original Message -----
From: Holger Gohlke <gohlke_at_scripps.edu>
Date: Thursday, August 7, 2003 3:22 pm
Subject: Re: AMBER: mpi in mm-pbsa

> Shuang Ding wrote:
> >
> > Dear Amber Users,
> >
> > When I use mm-pbsa to calculate free energy in amber7, I got
> this error
> > "mpirun must be used to launch all MPI applications
> > /usr/local/etc/amber7/exe/sander -O -i sander_rec.in -o
> sander_rec.1.out -c ../c1_rec.crd.1 -p ../x.top not successful"
> > I didn't find a way to apply mpirun in mm-pbsa input file. How
> can the mpirun be applied automatically when sander is used in mm-
> pbsa?
> A workaround should be to replace the line
> my $command = $r_pro->{"SANDER"} ...
> with
> my $command = "mpirun -np 1 " . $r_pro->{"SANDER"} ...
> in the functions calc_MM_GB_SAS and calc_NM in mm_pbsa.pl.
>
> Let me know if it still doesn't work.
>
> Best regards
>
> Holger
>
> >
> > Thanks a lot.
> >
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> --
> +++++++++++++++++++++++++++++++++++++++++++++
> Dr. Holger Gohlke
> Dept. of Molecular Biology, TPC15
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> La Jolla CA 92037 USA
> phone: +1-858-784-9788
> fax: +1-858-784-8896
> email: gohlke_at_scripps.edu
> +++++++++++++++++++++++++++++++++++++++++++++
> -------------------------------------------------------------------
> ----
> The AMBER Mail Reflector
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>
>

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