Running Simulation/Analysis

Running MD Simulation

To perform MD simulation using INP, the user executes spdyn with the following command, where mpirun and 8 CPU cores are used as an example:

$ mpirun -np 8 /home/user/genesis/bin/spdyn INP > md.log

The last “> md.log” means that log information of the MD simulation such as potential energy at each MD step is written in md.log. If “> md.log” is omitted, the log information is just displayed in the terminal. Output restart and trajectory filenames can be specified in input file, INP.

 In both spdyn and atdyn, hybrid MPI/OpenMP calculation is available, where MPI is mainly used for parallel computation between nodes (distributed memory), and OpenMP is used within the node (shared memory). For details, please refer to this page.

After the MD simulation is finished, the user will obtain trajectory file(s). Trajectory data of atomic coordinates can be visualized by molecular viewers such as VMD. Since the GENESIS program package does not provide any visualizers, users must prepare external viewers.

Running Analysis

GENESIS provides some useful trajectory analysis tools, which might also be installed in the bin directory. Usage of those executables is similar to that of atdyn or spdyn as mentioned above. The following commands are examples for trj_analysis, which analyzes distance, angle, and dihedral angle of selected atoms in the coordinates trajectory files.

$ /home/user/genesis/bin/trj_analysis INP

Like spdyn, the user must prepare a control file for trj_analysis, and the example control file can be automatically created by appending “-h ctrl” option as described in this page. Because trj_analysis is not parallelized with MPI protocols, we do not use mpirun when running trj_analysis. Please note that most analysis tools in GENESIS do not require mpirun, while some tools require it.  In addition, some tools like mbar_analysis can use OpenMP parallelization. Detailed usage of each tool can be found in the tutorials.