SPONGE in MindSpore is a high-performance and modularized molecular dynamics simulation library developed by `Yiqin Gao` group (`Peking University` and `Shenzhen Bay Laboratory`) and `MindSpore` team at `Huawei` Company. It can efficiently simulate traditional molecular dynamics tasks based on the “graph-kernel-fusion” and “automatic parallelization” features of MindSpore. In the meanwhile, it utilizes the automatic differentiation feature of MindSpore, and introduces machine learning methods, such as neural network, into traditional molecular simulation, achieving methodological inventions.
SPONGE in MindSpore is a molecular dynamics simulation library, featuring high performance and modularization. It is developed by the `Yiqin Gao` group (`Peking University` and `Shenzhen Bay Laboratory`) and `Huawei MindSpore` team. It can efficiently simulate traditional molecular dynamics tasks based on the "graph-kernel-fusion" and "automatic parallelization" features of MindSpore. In addition, it utilizes the automatic differentiation feature of MindSpore, and introduces machine learning methods, such as neural network, into traditional molecular simulation, achieving methodological inventions.
This example demonstrates how to perform high-performance molecular dynamics simulations with the built-in SPONGE module of MindSpore on `GPU`.
The following example demonstrates how to perform high-performance molecular dynamics simulations with the built-in MindSpore SPONGE module on a `GPU`.
## Dataset
## Dataset
There are three inputs for the example, property file `NVT_290_10ns.in`, topology file `WATER_ALA.parm7` and coordinates file `WATER_ALA_350_cool_290.rst7`, respectivelly.
There are three inputs in the example, the property file `NVT_290_10ns.in`, the topology file `WATER_ALA.parm7` and the coordinates file `WATER_ALA_350_cool_290.rst7`, respectivelly.
Topology file and coordinates file can be generated by `tleap` in `AmberTools` ([link](<http://ambermd.org/GetAmber.php>)). For more details, please refer to:
The topology file and coordinates file can be generated by `tleap` in `AmberTools` ([link](<http://ambermd.org/GetAmber.php>)). For more details, please refer to:
There are sorts of energy in the output, steps (_steps_), temperature (_TEMP_), total energy (_TOT_POT_E_), bond energy (_BOND_ENE_), angle energy (_ANGLE_ENE_), dihedral energy (_DIHEDRAL_ENE_), non bond enrgy, includes Coulomb force (_14CF_ENE_) and Leonard-Jones energy (_14LJ_ENE_), Van der Waals energy (_LJ_ENE_) and Coulomb force in PME (_CF_PME_ENE_).
There are sorts of energy in the output, steps (_steps_), temperature (_TEMP_), total energy (_TOT_POT_E_), bond energy (_BOND_ENE_), angle energy (_ANGLE_ENE_), dihedral energy (_DIHEDRAL_ENE_), non-bond energy, includes Coulomb force (_14CF_ENE_) and Lennard-Jones energy (_14LJ_ENE_), Van der Waals energy (_LJ_ENE_) and Coulomb force in PME (_CF_PME_ENE_).