ALIs
kommt nochAMBER - Assisted Model Building with Energy Refinement
AMBER refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos.
Assisted Model Building with Energy Refinement
"Amber" refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. The current version of the code is Amber version 11, which is distributed by UCSF subject to a licensing agreement described on the Amber home page. Essentially this means that you may use the software only for research and teaching purposes.
Versions installed on LRZ HPC systems
| Version | Platform |
|---|---|
| Amber 10 (parallel) | Altix 4700 (HLRB-II) and Opteron Linux Cluster |
| Amber 11 (parallel) | Altix 4700 (HLRB-II), sgi ICE and Opteron Cluster |
Usage of Amber on LRZ systems
Please load the appropriate environment module:
module load amber
This will enable you to run all available binaries for the loaded version of Amber. E. g., you can then call xleap or sander.
Notes:
leaprcfiles may be copied from$AMBERHOME/dat/leap/cmd- MPI parallel executables have the postfix
MPIe.g.,sander.MPI - with version 11, pmemd comes in two flavors: A serial
pemdbinary, and an MPI parallelpmemd.MPIbinary - likewise, version 11 allows the
nabprogram to run in parallel. This is done by setting OMP_NUM_THREADS to the number of threads one wishes to use.
Documentation and support
Please consult the Amber home page for documentation:
If the amber environment module is loaded, the environment variable $AMBER_DOC will point at a directory containing PDF documentation.
If you notice any problems with the LRZ installation of Amber, please contact LRZ HPC support.