Re: [AMBER] Running simulations in parallel

From: Jason Swails <>
Date: Mon, 25 Jan 2016 17:32:45 -0500

On Mon, Jan 25, 2016 at 1:19 PM, Aishani Prem <> wrote:

> Hi,
> I have been trying to run simulations in amber. When I used the
> command --
> mpirun -np 8 $AMBERHOME/bin/sander

​This won't work. sander is a serial program. You need to use
"sander.MPI" with mpirun.

> -O -i -o
> test_gb_md1_nocut.out -c test_gb_init_min.rst -p test.prmtop -r
> test_gb_md1_nocut.rst -x test_gb_md1_nocut.mdcrd.
> But this is not working and when I tried installing amber 14 in parallel
> using the command--
> ./configure -mpi gnu
> I get an error--
> IOError: [Errno 13] Permission denied:
> '.patches/AmberTools15_Unapplied_Patches/update.4'

​What is $AMBERHOME? Is it /usr/local? You need to have write permissions
in $AMBERHOME in order to compile it. The first time it tries to create a
file (in this case, during the update process), it fails with a permission

So your options are either

1) Use "chown" to change the ownership of $AMBERHOME to your username.
Something like this: "sudo chown -R `whoami` $AMBERHOME"

2) Install as root. I highly recommend NOT doing this. ESPECIALLY if you
are not a relative expert with Linux/Unix.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Jan 25 2016 - 15:00:03 PST
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