AMBER 8 is installed in /share/apps/amber8. Users will need to create a script to run their job, and then submit that script to the queue system. For parallel runs, use the mpich PE as noted in the Queue system page.
Here is an example of script that could be used to run a 4-CPU parallel sander job:
#!/bin/csh -f setenv AMBERHOME /share/apps/amber8 cd /home/username/amberjob /share/apps/mpich-1.2.7p1/bin/mpirun -nolocal -machinefile $TMPDIR/machines -np 4 \ $AMBERHOME/exe/sander -O -i job.in -o job.out -p job.prmtop \ -c job.restrt -r job.restrt -x job.mdcrd
To submit the script, use a command like the following:
qsub -pe mpich 4 scriptname