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[资源] 分子动力学计算软件NAMD

下载网址：
http://www.ks.uiuc.edu/Developme ... gi?PackageName=NAMD
介绍：
NAMD，用于在大规模并行计算机上快速模拟大分子体系的并行分子动力学代码。NAMD用经验力场，如Amber，CHARMM和Dreiding，通过数值求解运动方程计算原子轨迹。

【作者】 Theoretical and Computational Biophysics Group,University of Illinois at Urbana-Champaign (UIUC)

【语言版本】 English

【收费情况】免费

【用途】 NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using switched fast ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code.

Current NAMD Feature Summary:

Software Setup

Free to download and use. (Redistribution prohibited.)
Precompiled binaries provided for 12 popular platforms.
Installed at major NSF supercomputer sites.
Portable to virtually any platform with ethernet or MPI.
C++ source code and CVS access for modification.

Molecule Building

Reads X-PLOR, CHARMM, AMBER, and GROMACS input files.
Psfgen tool generates structure and coordinate files for CHARMM force field.
Efficient conjugate gradient minimization.
Fixed atoms and harmonic restraints.
Thermal equilibration via periodic rescaling, reinitialization, or Langevin dynamics.

Basic Simulation

Constant temperature via rescaling, coupling, or Langevin dynamics.
Constant pressure via Berendsen or Langevin Nose-Hoover methods.
Particle mesh Ewald full electrostatics for periodic systems.
Symplectic multiple timestep integration.
Rigid waters and bonds to hydrogen atoms.

Advanced Simulation

Chemical and conformational free energy calculations.
Locally enhanced sampling via multiple images.
Tcl based scripting and steering forces.
Interactive visual steering interface to VMD.

Scalable Performance

Based on the Charm++/Converse parallel runtime system.
Spatial data decomposition for limited communication pattern.
Message driven execution for latency tolerance on commodity networks.
Measurement-based load balancing for scaling to hundreds of processors.
Largest simulation to date is over 300,000 atoms on 1000 processors.

【相关链接】
　　美国伊利诺依大学：理论生物物理学研究组

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