AMBER Archive (2003)

Subject: Re: AMBER: mpi in mm-pbsa

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Thu Aug 07 2003 - 14:22:53 CDT

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
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