Usage of GENESIS

Notice/Assumption

  • Working on a typical Linux workstation
  • GENESIS executables are installed in /home/user/genesis/bin/.

For more practical details, please also check the tutorials. In the bottom of this page, you may find more specific instruction of GENESIS on cluster machines, specific supercomputers such as K computer or workstations with GPU cards.

Quick Usage

Input file template generation for MD; please check this page for further details.
# check control parameters of md
% /home/user/genesis/bin/spdyn -h ctrl md ← show input file template

# check all control parameters of md 
% /home/user/genesis/bin/spdyn -h ctrl_all md ← show detailed input file template
Running MD
# running MD with 8 MPI processes and 3 OpenMP threads (24 processes in total)
$ export OMP_NUM_THREADS=3
$ mpirun -np 8 /home/user/genesis/bin/spdyn INP > md.log
Input file template generation for analysis tool (rmsd_analysis for example)
# check control parameters of rmsd_analysis (same option works for other tools)
% /home/user/genesis/bin/rmsd_analysis -h ctrl
Running analysis tool (rmsd_analysis for example)
# running RMSD analysis
$ /home/user/genesis/bin/rmsd_analysis INP

if you add “-h ctrl” to the other executables in the bin directory, input file template will be shown just like the above example. If you run commands without arguments, you may find available command line options.

Detailed Information

Usage on specific computer systems

Some more detailed examples of the installation scheme of GENESIS, batch scripts for Hybrid MPI/OpenMP computation, GPGPU computation, and a command to submit a job for the following computer systems are available from the following link. If those example scripts do not work on your system, please check the user manual and error message carefully. Of course, you can ask at the forum. In that case, please write detailed information, such as OS (distribution), compiler versions, and error messages.