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.
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.
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
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.