Namd is a parallel molecular dynamics code designed for highperformance simulation of large biomolecular systems. Scalable molecular dynamics for large biomolecular systems. Nanoscale molecular dynamics namd is a parallel molecular dynamics application that has been used to make breakthroughs in understanding the structure and dynamics of large biomolecular complexes, such as viruses like hiv and various types of influenza. Flexibility and interoperability in a parallel molecular dynamics code postscript. Namd paper the physical concepts behind namd along with the programs design and algorithms are described in this publication that we recommend highly for study along with working through the above namd tutorial. Amd epyc processors bring a new balance to the datacenter. Scalable molecular dynamics 8 51,000 users, 2900 citations blue waters target application 2002 gordon bell award illinois petascale computing facility atp synthase psc lemieux computational biophysics summer school gpu acceleration nvidia tesla ncsa lincoln. Biomolecular reaction and interaction dynamics global. Namd uses the popular molecular visualization package vmd for simulation setup and trajectory analysis, but is also filecompatible with amber, charmm, and xplor. Of these, namd is regarded as the most scalable and the most efficient on highly parallel runs, although. Namd performance on xeonscalable 8180 and 8 gtx 1080ti gpus. Namd pioneered the use of hybrid spatial and force decomposition, a technique used by most scalable programs for biomolecular simulations, including blue matter and desmond which were described at supercomputing 2006. Phillips and others published scalable molecular dynamics with namd. Highperformance scalable molecular dynamics simulations.
Namd is one of the most efficient and scalable parallel molecular dynamics codes for largescale biomolecular simulations in the open source domain. Btrc for macromolecular modeling and bioinformatics beckman institute, uiuc. Scalable molecular dynamics with namd theoretical and. Namd scales to hundreds of processors on highend parallel platforms, as well as tens of processors on lowcost commodity clusters, and also runs on. Namd has an interface to quantum chemistry packages orca and mopac, as well as a scripted interface to many other quantum packages. Hirasaki and walter g chapman and dilipkumar asthagiri. Cray and the university of illinois at urbanachampaign. Pdf scalable molecular dynamics with namd james phillips. Scalable molecular dynamics with namd northwestern scholars. It explains the concepts and algortithms underlying modern molecular dynamics md simulations as realized in namd, e. They differ in how the force computations are assigned to processors. Namd is a portable parallel application for biomolecular simulations. Namd scales to hundreds of processors on highend parallel platforms, as well as tens of processors on lowcost commodity clusters, and also runs on individual desktop. Namd is a parallel molecular dynamics software designed for highperformance simulations of large biomolecular systems.
Vmd is a highperformance molecular graphics viewer, used for displaying molecular structures, viewing sequence information, and for structure generation and dynamic analysis. Strong scaling is necessary for molecular dynamics as problem size is fixed, and a large number of iterations need to be executed to. Namd nanoscale molecular dynamics is a production molecular dynamics md application for biomolecular simulations that include assemblages of proteins. Accelerated molecular dynamics simulations of ligand. The results reveal the factors that can inhibit scaling and performance efficiency on emerging multicore processors. This guide includes the capabilities of the program, how to use these capabilities, the necessary input les and formats, and how to run the program both. The fit of the bestscoring structures inside the density map was refined using the molecular dynamics flexible fitting mdff protocol trabuco et al. New structural insights into kir channel gating from. Namd namd, recipient of a 2002 gordon bell award and a 2012 sidney fernbach award, is a parallel molecular dynamics code designed for highperformance simulation of large biomolecular systems. Namd works with amber and charmm potential functions, parameters, and file.
Namd permitted simulation of a proteindna complex en compassing 36,000 atoms,5 one of the largest simulations car ried. Namd is the result of an interdisciplinary collaboration between prof. Unleashing the graphic processing unitsbased version of namd. Scalable molecular dynamics with namd on the summit system 1. This post will look at the molecular dynamics program, namd. One computationally efficient treatment is based on the classical drude oscillator in which an auxiliary charged particle is attached by a spring to each nucleus. Strategy for running molecular dynamics simulations this part of the lecture describes the general steps in setting and running molecular dynamics md simulations using namd for a short polyvaline peptide vvvv capped with acetyl and amide groups. Parallel machines provide the potential to meet this computational challenge. Scalable molecular dynamics with namd phillips 2005. Theoretical and computational biophysics group tcb. Pdf molecular dynamics simulations of nmr relaxation and. Namd is a parallel molecular dynamics software for biomolecular simulations.
It is noted for its parallel efficiency and is often used to simulate large systems millions of atoms. Scalable molecular dynamics with namd on the summit system. A coarsegrained molecular dynamics simulation using namd. With an objectbased hybrid force and spatial decomposition. Scalable algorithms for molecular dynamics simulations on cines. Modeling nanopores for sequencing dna the aksimentiev group. The following article on namd is directed to novices and experts alike. Jun 26, 2001 we present an optimized parallelization scheme for molecular dynamics simulations of large biomolecular systems, implemented in the productionquality molecular dynamics program namd. Namd is a parallel molecular dynamics code designed for high performance simulation of large biomolecular systems. 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. Namd, recipient of a 2002 gordon bell award and a 2012 sidney fernbach award, is a parallel molecular dynamics code designed for highperformance simulation of large biomolecular systems. This chapter provides stepbystep instructionsof how to build atomic scale models of biological and solidstate nanopore systems, use themolecular dynamics method to simulate the electric fielddriven transport of ions and dnathrough the nanopores, and analyze the results of such computational experiments. A comprehensive exploration of the conformational and energetic landscape. Oct 12, 2005 namd is a parallel molecular dynamics code designed for high.
Namd works with amber and charmm potential functions, parameters, and file formats. Molecular dynamics studies have also been performed 18,19, but the short simulation times hundreds of ns often make it difficult to observe the whole gating process. Using multiple time stepping can increase computational ef. The energy profile of selfassembly process of dlpe, dlps, dope, dops, dlipe, and dlips in water was investigated by a coarsegrained molecular dynamics simulation using namd package.
Phillips, rosemary braun, wei wang, james gumbart, emad tajkhorshid, elizabeth villa, christophe. Namd scales to hundreds of processors on highend parallel platforms, as well as tens of processors on lowcost commodity clusters, and also runs on individual desktop and laptop computers. To harness this potential, it is necessary to develop a scalable program. We have used the roccc compiler toolset to generate the circuit and implemented it on the sgi altix 4700. Md to understand the structure and function of biomolecules. A read is counted each time someone views a publication summary such as the title, abstract, and list of authors, clicks on a. A practical guide to molecular dynamics simulations of dna. Scalable molecular dynamics with namd on blue genel sameer kumar1, chao huang 2, gengbin zheng, eric bohm abhinav bhatele2, james c. Amd epyc processors help enable more performance, flexibility, and security performance. The molecular dynamics computation involves calculating forces on all atoms during.
A comprehensive exploration of the conformational and. Scalable molecular dynamics with namd wiley online library. Namd is a scalable molecular dynamics application, which has proven its performance on several parallel computer architectures. Phillips and others published scalable molecular dynamics with namd find, read and cite all the research you need on. More recent proposals for scalable molecular dynamics 8, 9, 10 use the basic strategy of hybrid decomposition, which originated from namd 2. Namd is a highly scalable parallel molecular dynamics simulator allowing for large scale modeling of cellular systems. Integrated with both industrystandard macromolecule design and ligand design tools, biovia discovery studio delivers a comprehensive, scalable portfolio of molecular simulation tools. Greater scalability for parallel molecular dynamics. The simulations for q23htt were performed using namd phillips et al. Molecular dynamics programs simulate the behavior of biomolecular systems, leading to understanding of their functions.
Pdf scalable molecular dynamics with namd on the summit. Molecular dynamics simulation of large biomolecular systems and long timescale biological phenomena requires tremendous computing power. Namd permitted simulation of a protein dna complex en compassing 36,000 atoms,5 one of the largest simulations car ried. Here, accelerated molecular dynamics amd is proposed to simulate processes of ligand binding to a gproteincoupled receptor gpcr, in this case the m3 muscarinic receptor, which is a target for treating many human diseases, including cancer, diabetes and obesity. Namd can be used on any machine from laptop to supercomputers running linuxunix, mac os x, or. The most cited manuscript is this category is scalable molecular dynamics with namd 49, which as observed is a work of computational chemistry.
The namd users guide describes how to run and use the various features of the molecular dynamics program namd. Parts of this infrastructure include generic force compu. Petascale molecular dynamics with namd center for scalable. Namd a parallel, objectoriented molecular dynamics software designed for highperformance simulation of large biomolecular systems millions of atoms developed by the joint collaboration of the theoretical and computational. Namd is a parallel molecular dynamics code designed for high. The official namd home page is located at tcbg namd research. With an objectbased hybrid force and spatial decomposition scheme, and an aggressive measurementbased predictive load balancing framework, we have attained speeds and speedups that are much higher than any reported.
Pdf scalable molecular dynamics with namd james phillips academia. Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending grzegorz nawrockia, wonpil imb,c, yuji sugitad,e,f, and michael feiga,f,1 adepartment of biochemistry and molecular biology, michigan state university, east lansing, mi 48824. Generalized scalable multiple copy algorithms for molecular. Pdf namd is a parallel molecular dynamics application that has been used to make breakthroughs in understanding the structure and. Scalable molecular dynamics with namd on the summit system abstract. Amd epyc 7002 series processors and namd molecular. Important questions exist regarding the quality of force fields used in molecular dynamics md simulations and their interoperable use with other available md implementations.
Namd is a widely used md simulation engine developed by key members of the proposed. This study presented proof that there were three major selfassembled arrangements which. Incorporating the influence of induced polarization in largescale atomistic molecular dynamics md simulations is a critical challenge in the progress toward computations of increased accuracy. Dec 01, 2005 namd is a parallel molecular dynamics code designed for high. Gromacs typically achieves superior performance on. It achieves best performance when there is a proper balance between cpu and gpu. Namd a parallel objectoriented molecular dynamics program pdf. Impact of multicores on largescale molecular dynamics. Namd namd, recipient of a 2002 gordon bell award and a 2012 sidney fernbach award, is a parallel molecular dynamics code designed for highperformance lecular systems. This peptide is one of the two peptides to be examined in the md project. Phillips, rosemary braun, wei wang, james gumbart, emad tajkhorshid, elizabeth villa, christophe chipot, robert d.
Schulten at the theoretical and computational biophysics group tcbg of beckman institute. Highperformance scalable molecular dynamics simulations of a. Scalable molecular dynamics david hardy urbana, illinois investigating free energy landscapes of membrane transport proteins through simulations on the alcf aurora supercomputer. A nave pairwise calculation of nonbonded forces between all pairs of atoms has a time complexity of on2. The selfassembly process was initiated from random configurations.
Namd has good gpu acceleration but is heavily dependent on cpu performance as well. Lightweight computational steering of very large scale. Scalable molecular dynamics with namd europe pmc article. In the present communication, we report the first implementation of a polarizable force field based on the classical drude oscillator model in the program namd.
Namd tools for scalable molecular dynamics information. Highperformance scalable molecular dynamics simulations of a polarizable force field based on classical drude oscillators in namd. Namd2 handles this problem in part by providing the infrastructure class hierarchy that embodies commonly needed molecular dynamics mechanisms. A portable and highly scalable program for biomolecular. Strong scaling is necessary for molecular dynamics as problem size is fixed, and a large number of iterations need to be executed to understand interesting biological phenomenon. Scalable algorithms for molecular dynamics simulations on. A comprehensive exploration of the conformational and energetic landscape of a rotaxane system. Namd scales to hundreds of processors on highend parallel platforms, as well as tens of processors on lowcost commodity clusters, and. Phillips and others published scalable molecular dynamics with namd find, read and cite all the research you need on researchgate. Outside of namd, we are experimenting with alternative ways to parallelize molecular dynamics computations. Scalable molecular dynamics with namd james phillips beckman institute, university of illinois.
Within the limits of memory and scalability, any simulation can be run on any number of processors. Together with visual molecular dynamics vmd and qwikmd, namds interface provides access to hybrid qmmm simulations in an integrated, comprehensive, customizable, and easytouse suite. Scalable molecular dynamics 51,000 users, 2900 citations blue waters target application 2002 gordon bell award illinois petascale computing facility atp synthase psc lemieux computational biophysics summer school gpu acceleration nvidia tesla ncsa lincoln. Namd is a parallel, objectoriented molecular dynamics code designed for highperformance simulation of large biomolecular systems. It scales from single computer up to hundreds of processors as highend parallel platforms. Comput chem find, read and cite all the research you need on researchgate. Scalable molecular dynamics with namd on blue genel. However, the computational complexity of such simulations is enormous. Force field validation for nucleic acid simulations. Greater scalability for parallel md 285 must correctly interleave the parallel communication logic.
A free powerpoint ppt presentation displayed as a flash slide show on id. This guide includes the capabilities of the program, how to use these capabilities, the necessary input. We present the foundations of biomolecular reaction and interaction dynamics global environment bridge developed on the galaxy platform that makes possible fundamental molecular dynamics of proteins through workflows and pipelines via commonly used packages, such as namd, gromacs and charmm. Scalable molecular dynamics with namd on blue genel umd. For scalable parallelism, namd employs a spatial decomposition of the atoms across a uniform threedimensional tessellation of space referred to as patches. The principal investigator is benoit roux from the university of chicago. With an objectbased hybrid force and spatial decomposition scheme, and an aggressive measurementbased predictive load balancing framework, we have attained speeds and speedups that are much higher than any.
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