Links
CHARMM-GUI
CHARMM-GUI is a web-based modeling support tool developed by the Im group at Lehigh University that automatically generates input files including initial structure of MD simulations for various MD software. GENESIS input files for not only MD simulations but also FEP calculations can be generated by CHARMM-GUI.
CafeMol
CafeMol is the MD simulation software for coarse-grained models developed by the Takada group at Kyoto University. They have developed a variety of coarse-grained models, and we have introduced some of them into GENESIS.
QSimulate
QSimulate-QM software developed by Quantum Simulation Technologies, Inc. is integrated with GENESIS (after ver. 1.6.1) to run QM/MM calculations. The software is highly parallelized and achieves high-throughput QM/MM-MD simulations at various levels of QM, DFTB3, DFT, MP2, etc. GENESIS/QSimulate-QM opens a broadened scope of applicability for QM/MM calculations. The use of the software has been demonstrated in a publication, J. Phys. Chem. B 125, 4701 (2021).