ProtoMol

ProtoMol is an object-oriented, component based, framework for molecular dynamics (MD) simulations. The framework supports the CHARMM 19 and 28a2 force fields and is able to process PDB, PSF, XYZ and DCD trajectory files. It is designed for high flexibility, easy extendibility and maintenance, and high performance demands, including parallelization. The technique of multiple time-stepping is used to improve long-term efficiency. The use of fast electrostatic force evaluation algorithms like Ewald, particle Mesh Ewald (PME), and Multigrid (MG) summation further enhances performance. Longer time steps are possible using MOLLY, Langevin Molly and Hybrid Monte Carlo, Nose-Hoover, and Langevin integrators. <b>Key Features of ProtoMol 3.0 (available Summer 2009):</b>1) Interface to OpenMM, an MD library with NVIDIA and ATI general purpose GPU support. OpenMM supports AMBER force fields and Generalized-Born implicit solvent. 2)Python bindings offered as MDLab, which allow for prototyping of high level sampling protocols, new integrators, and new force calculations in Python. 3) Coarse grained normal mode analysis (CNMA), which provides a scalable O(N9/5) time and O(N3/2) memory diagonalization. CNMA approximates low frequency modes very well.4) Normal Mode Langevin (NML) dynamics, which uses CNMA to periodically compute low frequency bases for propagation of dynamics, while fast modes are minimized to their equilibrium position. NML allows timesteps of 100 fs and more for even small proteins (> 30 residues) with real speedups that are about a third of the timestep used.5) Full checkpointing support, which simplifies use in distributed computing platforms such as Condor or Folding@Home. <br/><br/>This project includes the following software/data packages: <br/> <ul> <li> <a href="https://simtk.org/frs?group_id=397#pack_680">ProtoMol </a> : ProtoMol is an object-oriented component based framework for molecular dynamics simulations. </li> </ul>

ProtoMol是一款面向对象、基于组件的分子动力学（MD）模拟框架。该框架兼容CHARMM 19和28a2力场，并能处理PDB、PSF、XYZ和DCD轨迹文件。设计上注重高度的灵活性、易于扩展和维护，以及高性能需求，包括并行化。通过采用多重时间步进技术，提高了长期效率。运用快速电静电力评估算法如Ewald、粒子网格Ewald（PME）和多网格（MG）求和，进一步增强了性能。采用MOLLY、Langevin Molly和混合蒙特卡洛、Nose-Hoover以及Langevin积分器，可以实现更长的步长。<strong>ProtoMol 3.0（预计于2009年夏季发布）的关键特性：</strong>1) 接口至OpenMM，一款支持NVIDIA和ATI通用GPU的MD库。OpenMM支持AMBER力场和广义-伯恩隐式溶剂。2) 提供Python绑定作为MDLab，允许在Python中实现高级采样协议的原型设计、新的积分器和新的力计算。3) 粗粒度正常模式分析（CNMA），提供可扩展的O(N^9/5)时间和O(N^3/2)内存对角化。CNMA对低频模式进行了很好的近似。4) 正常模式Langevin（NML）动力学，利用CNMA定期计算低频基，以传播动力学，同时快速模式被最小化至其平衡位置。NML允许使用100 fs甚至更长的步长，即使是小蛋白（>30个残基）也能实现约三分之一步长的实际加速。5) 完全检查点支持，简化了在Condor或Folding@Home等分布式计算平台上的使用。<br/><br/>本项目包括以下软件/数据包：<br/><ul><li><a href="https://simtk.org/frs?group_id=397#pack_680">ProtoMol </a>：ProtoMol是一款面向对象、基于组件的分子动力学模拟框架。</li></ul>