This version contains a new feature and some fixes as follows.
- (spdyn) Cartesian coordinates can be employed as CV in the string method
- (rpath_generator) improved functionality
- (atdyn/spdyn) more smart handling of restart files
- (spdyn) show GPU hardware information in log file
- (spdyn) multiple GPUs in a single node can be used effectively in non-OpenMPI environment (such as Intel MPI)
structure_check is implemented in spdyn (runtime structure check upon pairlist generation)
- (atdyn) support CHARMM19
Please also check the updated usage page about GPUs.
International workshop entitled “Frontiers in Computational Biophysics and Biochemistry” will be held on Feb. 27-28, 2017. The major topics of the workshop are free-energy calculations, folding and aggregations, protein-protein interactions, and cellular-scale simulations. GENESIS hands-on tutorial will also be held on Feb. 28 – Mar. 1.
- Iksoo Chang (Daegu Gyeongbuk Institute of Science and Technology, Korea)
- Chris Chipot (University of Illinois, USA)
- Michael Feig (Michigan State University, USA)
- Giacomo Fiorin (Temple University, USA)
- Sihyun Ham (Sookmyung Women’s University, Korea)
- Nobuyuki Matubayashi (Osaka University, Japan)
- Kei-ichi Okazaki (Institute for Molecular Science, Japan)
- John E. Straub (Boston University, USA)
Check the website for the details of the workshop. Program is also available here.
Free of charge.
Please check the website and follow the guidance.
Tutorial materials will be available here.
This is a minor update release concerning the following issues.
- (code) fix problems while installing with CUDA-8.0RC and single precision
- (code) fix file I/O of the analysis tools (mbar_analysis, wham_analysis, pmf_analysis)
- (code) change default of pme_alpha in the [ENERGY] section
- (code) remove unnecessary error messages
- (tests) set pme_alpha in the control files due to change of the default
- (manual) fix sample of the [SELECTION] section (p.43)
The new version is available here!
Source code, manual, and test set is available at this page! New version is also installed in K computer.
The source code will be available at this site. User registration is no longer required to get GENESIS!
Check this page! The GENESIS 1.0 paper was selected as one of top 10 articles!
GENESIS 1.0 published on WIREs Comput. Mol. Sci. is available online.