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AmberOverviewAMBER (Assisted Model Building with Energy Refinement) is a general purpose molecular mechanics/dynamics suite which uses analytic potential energy functions,derived from experimental and ab initio data, to refine macromolecular conformations. AMBER version 7.0 is available on the Origin and Altix machines. AMBER version 8.0 has been ordered for the CSAR machines and will be placed on the system at the earliest opportunity. For a benchmark comparison of the improved speed of Amber 8 on an IBM SP2 machine see their benchmark page. Restrictions on UseThere are no restrictions on the use of the executable software for most CSAR users, however you will need to contact a member of the CSAR frontline team in order to be added to the access control list for the code. Any users of the CSAR service from for-profit organisations must have a signed licence agreement with the University of California, San Francisco in order to use the Amber software. Set Up ProcedureOnce you have been added to the access control list
you will be able to access Amber using the module
command. There may be several versions of Amber on the system at any
one time, each of which will have its own module. To see which versions
are available type Running the CodeThe versions of Amber on the CSAR Origin systems which
are loaded using modules containing the string mpirun -np 16 sander ...
The versions of Amber on the CSAR Origin systems which
are loaded using modules containing the string export OMP_NUM_THREADS=16 sander ...
The versions of Amber on the CSAR Altix system are
MPI codes and should therefore be launched using the Refer to the Amber manuals for further information on running the codes. Further InformationAMBER is fully described in the following manuals (pdf format): |
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Page maintained by csar-advice@cfs.ac.uk This page last updated: Thursday, 01-Dec-2005 13:37:40 GMT |