Amber 18

Amber (Assisted Model Building with Energy Refinement) refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules and a package of molecular simulation programs which includes source code and demos. AmberTools are also available with this release.

Accessing the software

To load the module:

$ module load Amber/18-foss-2018b-AmberTools-18-patchlevel-10-8

Or, to load the module with GPU support:

$ module load Amber/18-fosscuda-2018b-AmberTools-18-patchlevel-10-8

An example command to include in your job script:

 $ pmemd -O -i <input_file> -o <output_file> -p <prmtop> -c <inpcrd> -r <restrt>

Example: Serial Job

An example can be found at ${BB_EXAMPLES}/amber/serial/sbatch.sh. The example can be copied to a test directory and submitted to the batch system using sbatch.

$ cp -r ${BB_EXAMPLES}/amber/serial ~/amber-serial-test
$ cd ~/amber-serial-test

Edit the sbatch.sh script according to your needs, then do:

$ sbatch sbatch.sh

Example: MPI Job

An example can be found at ${BB_EXAMPLES}/amber/MPI/sbatch.sh. The example can be copied to a test directory and submitted to the batch system using sbatch.

$ cp -r ${BB_EXAMPLES}/amber/MPI ~/amber-mpi-test
$ cd ~/amber-mpi-test

Edit the sbatch.sh script according to your needs, then do:

$ sbatch sbatch.sh

Example: GPU Job

An example can be found at ${BB_EXAMPLES}/amber/GPU/sbatch.sh. The example can be copied to a test directory and submitted to the batch system using sbatch.

$ cp -r ${BB_EXAMPLES}/amber/GPU ~/amber-gpu-test
$ cd ~/amber-gpu-test

Edit the sbatch.sh script according to your needs, then do:

$ sbatch sbatch.sh

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

The following previous versions of Amber are available on this service:

Known Problems & Limitations

None.

Other Information

The Support Level for this application is An.

See the Amber website for more information about this application.

 


Last modified: 21 December 2018