Running CHARMM at ABCC

To run CHARMM you will need to apply for an account at ABCC or use the departmental account there (ask Mario Amzel about this). The following commands will setup Charmm (using C-shell):

source /usr/local/fbscapp/accelrys/cshrc

Then you have to define the variables that you will need for mpirun (MPI = Message Passing Interface).

set CHARMM=/usr/local/fbscapp/accelrys/I2000.1/mpi6m3/charmm.exe
set input="stream=your_input_file"

The stream is a work around the problem of rewinding the file when running in parallel. Your stream.inp file should look like this (you can find it in /usr/local/fbscapp/accelrys).

* CHARMM test stream file for parallel runs
*  where rewinding stdin is not possible
*
stream @stream
stop

The Charmm input file does not need to have anything particular to be run in parallel. You can the run the program using the following command (np is the number of processors you want to use). Note that the order of flags for the mpirun commands seems to matter. If you put '-cpr' after '-np 2' it won't work, but I do not know why.

mpirun -np 2 -cpr $CHARMM $input < stream.inp > your_output_file