Q1: What is GENESIS and what is its main purpose?

A: GENESIS (GENeralized-Ensemble SImulation System) is a suite of computer programs designed for conducting molecular dynamics (MD) simulations of biomolecular systems. Developed by the Computational Biophysics Research Team at RIKEN Center for Computational Science, it serves as an important research tool in structural and molecular biology, enabling simulations of biomolecules such as proteins, nucleic acids, lipids, and glycans.

Q2: What are the key features and capabilities of GENESIS?

A: GENESIS is a highly-parallel and multi-scale MD simulator that includes enhanced sampling algorithms for biomolecular and cellular simulations. It supports quantum mechanics / molecular mechanics (QM/MM), atomistic force fields (like CHARMM and AMBER) and various coarse-grained (CG) models. Its capabilities span basic MD simulations, energy minimization, and a wide range of advanced sampling methods, including Replica-Exchange Molecular Dynamics (REMD), Generalized replica-exchange with solute tempering (gREST), replica-exchange umbrella sampling (REUS), multi-dimensional REMD method, Gaussian accelerated Molecular Dynamics (GaMD), Reaction Path Search (RPATH), and Cryo-EM flexible fitting. GENESIS is optimized for high performance on modern supercomputers, utilizing hybrid MPI+OpenMP parallelism and GPGPU acceleration, and features parallel I/O for extremely large systems. Refer to GENESIS Functions for more details.

Q3: What are the system requirements for installing GENESIS?

A: To install GENESIS, you need a Fortran compiler (such as gfortran, ifort, or frtpx) and a preprocessor (cpp, fpp, or frtpx). For parallel computing, MPI libraries (like OpenMPI, Intel MPI, or Fujitsu MPI) are essential, while OpenMP is generally supported by modern Fortran compilers. GENESIS can be installed on Linux, macOS, and Windows 10/11 operating systems. A full list of requirements can be found here.

Q4: Where can I find detailed installation instructions and user documentation?

A: Comprehensive installation steps, including system requirements and troubleshooting tips, are provided in Chapter 2 of the GENESIS User Guide and this page. The source code and regression test sets are available for download from the GENESIS repository on Github. Additionally, online tutorials for basic MD simulations, enhanced sampling, and various analyses can be found on this page. You can also generate a template control file for any GENESIS program by executing the program with the -h ctrl option (e.g., spdyn -h ctrl md).

Q5: How do I prepare input files for GENESIS simulations?

A: To run MD simulations with GENESIS, you need to prepare input files that define the initial structure’s coordinates, system topology, and force field parameters. GENESIS supports input file formats from various common MD software, including CHARMM, AMBER, and GROMACS. Typically, essential input files consist of a topology file (topfile, prmtopfile, or grotopfile), a parameter file (parfile), and a structure/coordinate file (psffile, pdbfile, crdfile, ambcrdfile, or grocrdfile). These files are usually generated using external setup tools such as VMD/PSFGEN, CHARMM-GUI, LEaP, or SMOG/SMOG2 servers. CG input files can be generated using GENESIS-cg-tool. Check our Tutorials for more information.

Q6: What analysis tools are available in GENESIS?

A: GENESIS offers a comprehensive suite of trajectory analysis tools. These include programs for analyzing center of mass coordinates (comcrd_analysis), diffusion constant (diffusion_analysis), hydrogen bonds (hb_analysis), membrane thickness (lipidthick_analysis), mean-square displacement (MSD) (msd_analysis), RMSD (rmsd_analysis), and various other structural and dynamic properties. It also provides tools for free energy analysis, such as WHAM (wham_analysis) and MBAR (mbar_analysis). There is also specialized SPANA tools for large-scale parallel analyses. Refer to the GENESIS User Guide (Section 3.2 Analysis tools) for more details.

Q7: Is GENESIS free software, and what are its citation requirements?

A: Yes, GENESIS is free software distributed under the terms of the GNU Lesser General Public License (LGPL) version 3 for versions 1.5 and later, and GNU General Public License (GPL) version 2 for 1.4 and earlier versions. Please refer to this page for the requirements of citation.

Q8: Are there any known limitations or common issues users should be aware of?

A: As a relatively new MD simulation program, GENESIS may still contain defects or bugs, so users are advised to carefully verify simulation results. Common installation problems often stem from missing compilers, MPI libraries, or mathematical libraries, or from incorrectly set environment paths. During simulations, frequently encountered issues include:

  • SHAKE algorithm convergence failures: often due to insufficient equilibration, problematic initial structures, or inappropriate input parameters.
  • Atomic clashes: where atom pairs are too close, leading to numerical errors. This can occur in initial structures or due to periodic boundary conditions.
  • Domain and cell definition issues in SPDYN: indicating that the number of MPI processors is unsuitable for the system size. Solutions often involve reducing the number of MPI processors, adjusting pairlistdist, or rebuilding a larger system.

Feel free to open a GitHub Issue for questions and bug reports.

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