AMBER 11

Basic Install Details

• The software was installed with Intel Compilers 11.1 and Openmpi 1.4.3.
• AmberTools 1.4 is patched to bugfix level 16.
• Amber 11 is patched to bugfix level 12.

Restrictions on use

This software is licensed for University of Manchester users. All users should familiarise themselves with the License Agreement before using this software. A copy is also available in $AMBERHOME/amber11.license.html .

Set up procedure

You can access Amber 11 and set up your user environment with the following command:

module load apps/intel-11.1/amber/11

Note: this loads additional modules required to run amber, i.e. mpi/intel-11.1/openmpi/1.4.3, compilers/intel/c/11.1.075 and compilers/intel/fortran/11.1.064, therefore unloading the amber module will also unload these additional modules.

Running the application

After loading the modulefile you need to have a batch job submission script. Below are some examples.

Serial Amber

1. Make sure you have the module loaded.

2. An example batch submission script:

### SGE Job Stuff
### Set the directory you submit from to be the working directory
#$ -cwd
### Inherit the user environment settings from the login node (important so the job can find all commands)
#$ -V

$AMBERHOME/exe/sander -O 
          -i file.in
          -o file.out
          -c file.restart
          -r file.rst
          -p file.prmtop
          -x file.cmd
          -inf file.inf

3. Submit with the command: qsub scriptname

Parallel Amber

1. Make sure you have the module loaded.

2. An example batch submission script:

### SGE Job Stuff
### Set the directory you submit from to be the working directory
#$ -cwd
### Inherit the user environment settings from the login node (important so the job can find all commands)
#$ -V
### Submit to the smp.pe and tells SGE how many processors are required. $NSLOTS picks up this number.
#$ -pe smp.pe 12

mpiexec -n $NSLOTS $AMBERHOME/exe/sander.MPI -O 
          -i file.in
          -o file.out
          -c file.restart
          -r file.rst
          -p file.prmtop
          -x file.cmd
          -inf file.inf

3. Submit with the command: qsub scriptname

• If you wish to run on more than 12 cores please contact us for advice on how best to submit your job (Do not follow the amber 12 instructions as the two versions differ).
• Please ensure that when running parallel amber you have selected the correct executable – normally with .MPI at the end of the name. Running a serial executable with multiple cores is inefficient and may give inaccurate results. If you in doubt about whether the part of amber you wish to use can be run in parallel please check the amber manual.

Further info

• Manuals are available on the system ($AMBERHOME/doc)
• The Amber web site also has manuals, tutorials, an FAQ and mailing list: