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To run this software interactively in a Linux environment run the commands:
module load desmond maestro
Note: do not load the schrodinger module; if you load that one, the desmond module will not work. If you load the schrodinger module in your .bashrc file, you will need to unload the module first:
module unload schrodinger
There are two distinctly different version of Desmond. The common version is distributed in binary form from D.E. Shaw and is bundled with Maestro. A second version is available on Itasca. This version is built from source and links many system libraries, resulting in a code that can scale to thousands of processors for some inputs. This build doesn't contain Maestro or many of the analysis features in the binary-distributed version. This 'from source' build is the default on Itasca, although the GUI enabled Maestro version can be loaded as well (desmond/2010-01).
#!/bin/bash -l #PBS -l walltime=01:00:00,pmem=500MB,nodes=256:ppn=8 #PBS -m abe cd $PBS_O_WORKDIR module load desmond/126.96.36.199 orterun -np 1024 mdsim --include apoa1.cfg --cfg \ boot.file=apoa1.dms --destrier mpi > apoa1.1024.log
Help and tutorials are available by selecting the "Help" menu within Maestro.