Description
Amber is the collective name for a suite of programmes that allow users to carry out molecular dynamic simulations.
Version
Amber version 9.0 is installed on ngs.wmin.ac.uk with all the patches released up to 08/06/2007 (bug fixes 1-35).
Documentation
The User's Manuals for Amber 9 can be found here.
Running Amber on the NGS (RAL node)
In what follows, we show how you can submit serial and parallel jobs on the NGS Westminster node via gsissh . Alternatively, AMBER jobs can be easily submitted through GEMLCA/P-Grade Portal.
The string 'xxx' in the subsequent commands is to be replaced with your id on NGS.
You can also create a directory within your home directory (named amber in the following examples) which will be the working directory.
Any input files required should be copied on the RAL node (using gsiscp ) in the appropriate directory ( /home/xxx/amber in our example).
Running Amber 9.0 on ngs.wmin.ac.uk :
- To submit a serial job on ngs.wmin.ac.uk , i.e., sander use the following command (one line):
globusrun -b -r ngs.wmin.ac.uk/jobmanager-lsf \
'&(jobtype=single)(executable=/usr/ngs/AMBER_9_0)\
(arguments=sander -O -i in.md -c crd.md.23 -o cytosine.out)'
To run the above examples, one should copy in his/her home or working directory all the input files required, which can be found in the /apps/amber/examples/serial_example and /apps/amber/examples/parallel_example directories respectively.
Useful Links
Amber Home Page
The Amber Mail Reflector
Compilation
Amber was compiled using:
- PGI 6.2 Compilers.
- Scali MPI Libraries.
- Amber supplied lapack and blas Libraries.
Bug fixes 1-35 are applied.
Contact
University of Westminster cannot offer any scientific support for this package. However, if you believe there is a problem with the installation please contact the NGS helpdesk.
