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Usage of Amber on JUROPA/HPC-FF

Amber is available on JUROPA/HPC-FF in

/usr/local/amber

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

/usr/local/amber/$version/example/pmemd

Examples of input files can be found in the subdirectories of

/usr/local/ADF/$version/examples

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


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