What is AMBER?
Assisted Model Building with Energy Refinement (AMBER) is a suite of biomolecular simulation programs comprising numerous programs to setup, perform and analyze molecular dynamic simulations. The name AMBER also refers to a series of classical molecular mechanics force fields, primarily designed for the simulation of biomolecules. For more details, please consult the AMBER Home page.
AMBER is distributed by UCSF in two parts: AmberTools (which is free of charge and released under the GPL licence) and Amber (which not only builds on AmberTools by adding
pmemd but is also distributed with a seperate license and fee structure). Essentially, this means that you may use the software only for research and teaching purposes.
build molecules, run MD or apply distance geometry restraints using generalized Born, Poisson-Boltzmann or 3D-RISM implicit solvent models
create force fields for general organic molecules and metal centers
preparatory tools for Amber simulations
semiempirical and DFTB quantum chemistry program
numerical solutions to Poisson-Boltzmann models
integral equation models for solvation
molecular dynamic simulations
pushing the boundaries of Amber MD, primarily through parameter fitting.
analyzing structure and dynamics in trajectories
energy-based analyses of MD trajectories
Note: MPI parallel executables have the postfix
sander in AmberTools,
pmemd in Amber facilitates much faster molecular dynamic simulations on parallel CPU or GPU hardware. On LRZ systems, both serial (
pmemd) and MPI parallel (
pmemd.MPI) versions of
pmemd are available. In addition,
pmemd can be compiled as a binary with CUDA (
pmemd.cuda) and/or CUDA and MPI (
pmemd.cuda.MPI) support on parallel GPU hardware such as DGX-1.
Usage of AMBER at LRZ
The environment modules package controls access to the software. Use "module avail amber" to find all available versions of AMBER installed at LRZ.
To use the default version of AMBER, please type:
> module load amber
This will enable you to run all available binaries for the loaded version of AMBER. E.g., you can then call
leaprc files may have to be copied from
$AMBERHOME/dat/leap/cmd to the current working directory.
Setting Up Batch Jobs
For productive-level molecular dynamic simulations using
pmemd.MPI, a SLURM batch job should be submitted via "sbatch". The example batch scripts provided in this section require the input files mdin.in, topology.prmtop and coordinates.inpcrd, all contained in the example archive, to be placed in ~/mydir before the run.
#!/bin/bash #SBATCH -o /dss/dsshome1/<group>/<user>/mydir/%x.%j.out
Note: Other AMBER binaries compiled with MPI support (e.g.,
sander.MPI) can be run by analogy.
Using Amber with DFTB
It is possible to run QM/MM AMBER calculations using the density functional tight binding method. To enable this, please proceed as follows.
First step (done in an interactive login shell):
> cd $HOME > mkdir -p my_amber/dat/slko > cd my_amber > module load amber > ln -s $AMBERHOME/exe > cp <your DFTB files> dat/slko
Second step (adjust batch script):
module load amber export AMBERHOME=$HOME/my_amber export PATH=$AMBERHOME/exe:$PATH
Note that various sets of DFTB files exist, and the file names partially overlap. You will need to set up multiple such installations if you want to use either different builds of amber (e.g. cm2, SuperMuc-NG) or different DFTB file sets.
Please consult the AMBER Home page for documentation. The AMBER Reference Manuals are either available at the AMBER Home page or via the the environment variable
$AMBER_DOC which points to a directory containing the PDF documentation.
If you have any questions or problems with AMBER installed on different LRZ platforms, please don't hesitate to contact LRZ HPC support staff.