AMBER

Search Software

AMBER. Assisted Model Building with Energy Refinement. AMBER refers to two things: a molecular mechanical force field for the simulation of biomolecules (which is in general use in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.

SW Documentation: 

To run this software interactively in a Linux environment run the command:

module avail amber

and choose the most recent version of the software applicable to your research. The exact name of the module will vary from machine to machine, and over time with new updates so be sure to study the list printed with the 'module avail' command demonstrated above. For example,

module load amber/11
The amber module requires and will automatically load several other modules. Pay attention to any error messages or warnings that result from loading the module as conflicts with other packages already loaded in your environment are a common source of error. An example submission script is below. Note that the #PBS lines need to be tuned for each cluster's policies. You may not need to run short jobs through the queue, so the program can be used interactively by loading the module and running the executable directly at the command prompt.
#!/bin/bash -l 
#PBS -l walltime=24:00:00,mem=16gb,nodes=2:ppn=8 
#PBS -m abe 

module load amber 

cd $PBS_O_WORKDIR 

mpirun sander.MPI -O -i AMP2md39.in -o AMP2md39.out -p \
  AMP2_wat.prmtop -c AMP2md38.rst -r AMP2md39.rst -x \
  AMP2md39.mdcrd
Amber 11 is available on Itasca. Calling the sander.MPI binary on more than one node (8 cores) requires the amber module to be loaded in your .bashrc file. If you are running pmemd.MPI this step is not necessary. A sample job script is below.
#!/bin/bash -l
#PBS -l walltime=8:00:00,pmem=1000mb,nodes=8:ppn=8
#PBS -m abe

module load amber/11

cd $PBS_O_WORKDIR

mpirun -np 64 -hostfile $PBS_NODEFILE `which pmemd.MPI` \
  -O -i mdin -c eq200.x -o cellulose.sander.log

Additional Documentation

 

Short Name: 
amber
SW Module: 
amber
Service Level: 
Ancillary