# mintsponge

**Repository Path**: dechin/mintsponge

## Basic Information

- **Project Name**: mintsponge
- **Description**: MindSponge分子动力学模拟软件的mint算子开发版本
- **Primary Language**: Python
- **License**: Apache-2.0
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2025-06-03
- **Last Updated**: 2026-04-28

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# mintsponge
MindSponge分子动力学模拟软件的mint算子开发版本

## 水分子体系能量极小化
```python
from mintsponge import Molecule, ForceField, Sponge
from mintsponge import set_global_units
from SpongeExt.backends import optim

set_global_units('nm', 'kj/mol')
system = Molecule(template='water.spce.yaml')
system.reduplicate([0.3, 0, 0])
new_sys = system.copy([0, 0, -0.3])
system.append(new_sys)
potential = ForceField(system, parameters='SPCE')
opt = optim.Adam(system.parameters(), 1e-3)
mini = Sponge(system, potential, opt)
mini.run(200, print_interval=20)
```

## 蛋白体系能量极小化
```python
from mintsponge import Sponge, ForceField, set_global_units
from mintsponge.system import Protein
from mintsponge.optimizer import SteepestDescent
from mintsponge.callback import WriteH5MD
set_global_units('nm', 'kj/mol')

system = Protein(pdb='./data/case1.pdb', rebuild_hydrogen=True)
energy = ForceField(system, 'AMBER.FF14SB')
min_opt = SteepestDescent(system.parameters(), 1e-7)
cb_h5md = WriteH5MD(system, 'p01.h5md', save_freq=10, write_image=False)
md = Sponge(system, energy, min_opt, write_h5md=cb_h5md)
md.run(500, print_interval=10, write_interval=10)
```

## 分子动力学模拟
```python
from mintsponge import Molecule, ForceField, Sponge, UpdaterMD, WithEnergyCell
from mintsponge.function import VelocityGenerator
from SpongeExt.backends import optim

system = Molecule(template='water.tip3p.yaml')
system.set_pbc_box([0.4, 0.4, 0.4])
system.repeat_box([5, 5, 5])

potential = ForceField(system, parameters=['TIP3P'], use_pme=True)

opt = optim.Adam(system.parameters(), 1e-3)

sim = WithEnergyCell(system, potential)
mini = Sponge(sim, optimizer=opt)
mini.run(500, print_interval=50)

temp = 300
vgen = VelocityGenerator(temp)
velocity = vgen(system.shape, system.atom_mass)

nvt = UpdaterMD(
    system=system,
    time_step=1e-3,
    velocity=velocity,
    integrator='velocity_verlet',
    temperature=300,
    thermostat='langevin',
)
md = mini.change_optimizer(nvt)
md.run(2000, print_interval=20)

npt = UpdaterMD(
    system=system,
    time_step=1e-3,
    velocity=velocity,
    integrator='velocity_verlet',
    temperature=300,
    pressure=1,
    thermostat='langevin',
)
md.change_optimizer(npt)
md.run(2000, print_interval=20)

print('The final pbc box is: {}'.format(system.pbc_box))
```