Usage
In the GENESIS program package, not only MD simulators but also various trajectory analysis tools are available. The users execute those programs on command line. Here, we briefly explain how to execute them. The users may find other useful information in the online Tutorial for practical usage, and also user manual for basic usage (see Chapters “Getting started” and “Available programs”).
General usage of the MD simulators (atdyn/spdyn)
The GENESIS program package contains two MD simulators: atdyn and spdyn. In most cases, atdyn is applied to small systems or coarse-grained systems. On the other hand, spdyn is mainly employed for large systems (> 100,000 atoms) in a periodic boundary condition. Basic usage of atdyn and spdyn is almost same, and it is displayed by executing the program with the “-h” option.
# Show the usage of spdyn
$ /home/user/genesis/bin/spdyn -h
Template input (or control) file of atdyn/spdyn can be obtained with the “-h ctrl” or “-h ctrl_all” option. If the users want to use spdyn for MD simulations, the following command is executed to generate a template control file:
# Generate a template control file for MD
$ /home/user/genesis/bin/spdyn -h ctrl_all md > INP
$ less INP
Then, the users edit this control file by themselves according to the user’s desired simulation condition. Note that in one line of the file all characters after “#” are recognized as a comment (not read in the program). Example control files are shown in Samples and Tutorials. In order to run the MD simulation, the users execute atdyn/spdyn for the control file. In the following example, MD simulation is carried out with 16 CPU cores, where the 4 MPI processors and 4 OpenMP threads are employed for parallel calculation:
# Run spdyn for INP using 16 CPU cores with mpirun
$ export OMP_NUM_THREADS=4
$ mpirun -np 4 /home/user/genesis/bin/spdyn INP > log
General usage of the trajectory analysis tools
The GENESIS program package contains various trajectory analysis tools (e.g., rmsd_analysis for the RMSD calculation, trj_analysis for the distance calculation, and so on). Basic usage of these tools is similar to that in the MD simulators, and it is displayed by executing the program with the “-h” option. For example, in the case of rmsd_analysis, the following command is executed:
# Generate a template control file of rmsd_analysis
$ /home/user/genesis/bin/rmsd_analysis -h ctrl > INP
$ less INP
Then, the users edit this control file by themselves according to the user’s desired condition. Example control files are shown in Tutorials. In order to run the analysis, the users execute the tool for the control file.
# Run RMSD analysis
$ /home/user/genesis/bin/rmsd_analysis INP > log
Note that MPI is disable in most analysis tools, while OpenMP parallelization is enable in some tools (e.g., wham_analysis and mbar_analysis).
Usage on specific computer systems
Here, we provide 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.