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Usage of Amber on JUROPA/HPC-FF

Amber is available on JUROPA/HPC-FF in


and can be accessed using

module load amber/<version>

where <version> is one of the following:

  • 10
  • 11
  • 11-1.5

AmberTools version 1.4 are available with Amber version 11 as well and are installed with MPI support where applicable (e.g. nab, ptraj). The path to the Amber root directory is $AMBERHOME. An example input for the pmemd module of amber can be found in


Examples of input files can be found in the subdirectories of


In order to run the example with Amber 11 copy all files into a local directory and submit the jobscript below with

msub water.js

#Example for the pmemd module of the Amber package
#MSUB -l nodes=1:ppn=8
#MSUB -l walltime=00:15:00
#MSUB -v tpt=1

module load amber/11

mpiexec -np 8 --exports=AMBERHOME \
$AMBERHOME/bin/pmemd -O -i water.inp \
-c water.coo -o water.out