NAMD: a Parallel, Object-Oriented Molecular Dynamics Program (original) (raw)

NAMD Molecular Dynamics Software Non-Exclusive, NonCommercial Use License

2000

The NAMD User's Guide describes how to run and use the various features of the molecular dynamics program NAMD. This guide includes the capabilities of the program, how to use these capabilities, the necessary input files and formats, and how to run the program both on uniprocessor machines and in parallel.

Scalable molecular dynamics with NAMD

Journal of Computational Chemistry, 2005

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in Cϩϩ and based on Charmϩϩ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

Scalable molecular dynamics on CPU and GPU architectures with NAMD

The Journal of Chemical Physics

NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU-and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics, controlling the temperature, pressure and pH, applying external potentials on tailored grids, leveraging massively parallel resources in multiple-copy simulations, as well as hybrid QM/MM descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations, and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts towards achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.

NAMD2: Greater Scalability for Parallel Molecular Dynamics

Journal of Computational Physics, 1999

Molecular dynamics programs simulate the behavior of biomolecular systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scalable program. It is also necessary that the program be easily modified by applicationdomain programmers. The NAMD2 program presented in this paper seeks to provide these desirable features. It uses spatial decomposition combined with force decomposition to enhance scalability. It uses intelligent periodic load balancing, so as to maximally utilize the available compute power. It is modularly organized, and implemented using Charm++, a parallel C++ dialect, so as to enhance its modifiability. It uses a combination of numerical techniques and algorithms to ensure that energy drifts are minimized, ensuring accuracy in long running calculations. NAMD2 uses a portable run-time framework called Converse that also supports interoperability among multiple parallel paradigms. As a result, different components of applications can be written in the most appropriate parallel paradigms. NAMD2 runs on most parallel machines including workstation clusters and has yielded speedups in excess of 180 on 220 processors. This paper also describes the performance obtained on some benchmark applications.

NAMD2: Greater Scalability for Parallel Molecular Dynamics* 1

Journal of …, 1999

Molecular dynamics programs simulate the behavior of biomolecular systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this ...

OOPSE: An object‐oriented parallel simulation engine for molecular dynamics

Journal of …, 2005

Preface OOPSE is a new molecular dynamics simulation program which is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded atom method (EAM) potential included in the code. Parallel simulations are carried out using the force-based decomposition method. Simulations are specified using a very simple C-based metadata language. A number of advanced integrators are included, and the basic integrator for orientational dynamics provides substantial improvements over older quaternion-based schemes.

ProtoMcol: A Molecular Dynamics Research Framework for Algorithmic Development

Lecture Notes in Computer Science, 2003

This paper describes the design and evaluation of ProtoMol, a high performance object-oriented software framework for molecular dynamics (MD). The main objective of the framework is to provide an efficient implementation that is extensible and allows the prototyping of novel algorithms. This is achieved through a combination of generic and object-oriented programming techniques and a domain specific language. The program reuses design patterns without sacrificing performance. Parallelization using MPI is allowed in an incremental fashion. To show the flexibility of the design, several fast electrostatics (N-body) methods have been implemented and tested in ProtoMol. In particular, we show that an O(N) multi-grid method for N-body problems is faster than particlemesh Ewald (PME) for N > 8, 000. The method works in periodic and nonperiodic boundary conditions. Good parallel efficiency of the multi-grid method is demonstrated on an IBM p690 Regatta Turbo with up to 20 processors for systems with N = 10 2 , 10 4 and 10 6. Binaries and source code are available free of charge at http://www.nd.edu/˜lcls/protomol.

Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system

IBM Journal of Research and Development, 2000

NAMD (nanoscale molecular dynamics) is a production molecular dynamics (MD) application for biomolecular simulations that include assemblages of proteins, cell membranes, and water molecules. In a biomolecular simulation, the problem size is fixed and a large number of iterations must be executed in order to understand interesting biological phenomena. Hence, we need MD applications to scale to thousands of processors, even though the individual timestep on one processor is quite small. NAMD has demonstrated its performance on several parallel computer architectures. In this paper, we present various compiler optimization techniques that use single-instruction, multiple-data (SIMD) instructions to obtain good sequential performance with NAMD on the embedded IBM PowerPCt 440 processor core. We also present several techniques to scale the NAMD application to 20,480 nodes of the IBM Blue Gene/Le (BG/L) system. These techniques include topology-specific optimizations to localize communication, new messaging protocols that are optimized for the BG/L torus, topology-aware load balancing, and overlap of computation and communication. We also present performance results of various molecular systems with sizes ranging from 5,570 to 327,506 atoms.

Wordom: a program for efficient analysis of molecular dynamics simulations

Bioinformatics, 2007

Wordom is a versatile program for manipulation of molecular dynamics trajectories and efficient analysis of simulations. Original tools in Wordom include a procedure to evaluate significance of sampling for principal component analysis as well as modules for clustering multiple conformations and evaluation of order parameters for folding and aggregation. The program was developed with special emphasis on user-friendliness, effortless addition of new modules and efficient handling of large sets of trajectories. Availability: The Wordom program is distributed with full source code (in the C language) and documentation for usage and further development as a platform-independent package under a GPL license from