Namd is a scalable molecular dynamics application, which has proven its performance on several parallel computer architectures. Namd tools for scalable molecular dynamics information. Within the limits of memory and scalability, any simulation can be run on any number of processors. Namd has an interface to quantum chemistry packages orca and mopac, as well as a scripted interface to many other quantum packages. This post will look at the molecular dynamics program, namd. Scalable molecular dynamics with namd on the summit system.
To harness this potential, it is necessary to develop a scalable program. Schulten at the theoretical and computational biophysics group tcbg of beckman institute. Namd has good gpu acceleration but is heavily dependent on cpu performance as well. 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. Integrated with both industrystandard macromolecule design and ligand design tools, biovia discovery studio delivers a comprehensive, scalable portfolio of molecular simulation tools. Impact of multicores on largescale molecular dynamics.
A coarsegrained molecular dynamics simulation using namd. Pdf scalable molecular dynamics with namd james phillips academia. Namd is a widely used md simulation engine developed by key members of the proposed. A practical guide to molecular dynamics simulations of dna. The results reveal the factors that can inhibit scaling and performance efficiency on emerging multicore processors. 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. Unleashing the graphic processing unitsbased version of namd. 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 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. Highperformance scalable molecular dynamics simulations of a. Scalable molecular dynamics with namd james phillips beckman institute, university of illinois. 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. Gromacs typically achieves superior performance on. Comput chem find, read and cite all the research you need on researchgate.
Using multiple time stepping can increase computational ef. Pdf scalable molecular dynamics with namd on the summit. The namd users guide describes how to run and use the various features of the molecular dynamics program namd. The following article on namd is directed to novices and experts alike. Scalable algorithms for molecular dynamics simulations on cines. 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. Amd epyc processors help enable more performance, flexibility, and security performance.
For scalable parallelism, namd employs a spatial decomposition of the atoms across a uniform threedimensional tessellation of space referred to as patches. A comprehensive exploration of the conformational and. Phillips, rosemary braun, wei wang, james gumbart, emad tajkhorshid, elizabeth villa, christophe. 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. Md to understand the structure and function of biomolecules.
Scalable molecular dynamics with namd theoretical and. Namd works with amber and charmm potential functions, parameters, and file formats. 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 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. The fit of the bestscoring structures inside the density map was refined using the molecular dynamics flexible fitting mdff protocol trabuco et al. Namd is the result of an interdisciplinary collaboration between prof.
Outside of namd, we are experimenting with alternative ways to parallelize molecular dynamics computations. It is noted for its parallel efficiency and is often used to simulate large systems millions of atoms. Namd permitted simulation of a proteindna complex en compassing 36,000 atoms,5 one of the largest simulations car ried. Important questions exist regarding the quality of force fields used in molecular dynamics md simulations and their interoperable use with other available md implementations. 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. 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. It scales from single computer up to hundreds of processors as highend parallel platforms. Namd is a parallel molecular dynamics code designed for high performance simulation of large biomolecular systems. Namd is a portable parallel application for biomolecular simulations. Lightweight computational steering of very large scale. Modeling nanopores for sequencing dna the aksimentiev group.
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. 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. A free powerpoint ppt presentation displayed as a flash slide show on id. A comprehensive exploration of the conformational and energetic landscape of a rotaxane system. Flexibility and interoperability in a parallel molecular dynamics code postscript. Btrc for macromolecular modeling and bioinformatics beckman institute, uiuc. A nave pairwise calculation of nonbonded forces between all pairs of atoms has a time complexity of on2. Force field validation for nucleic acid simulations. Pdf namd is a parallel molecular dynamics application that has been used to make breakthroughs in understanding the structure and. Highperformance scalable molecular dynamics simulations of a polarizable force field based on classical drude oscillators in namd.
Scalable molecular dynamics with namd on blue genel. A comprehensive exploration of the conformational and energetic landscape. Vmd is a highperformance molecular graphics viewer, used for displaying molecular structures, viewing sequence information, and for structure generation and dynamic analysis. Phillips, rosemary braun, wei wang, james gumbart, emad tajkhorshid, elizabeth villa, christophe chipot, robert d. Highperformance scalable molecular dynamics simulations. Scalable algorithms for molecular dynamics simulations on. Namd is a parallel molecular dynamics software for biomolecular simulations. 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 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.
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 is one of the most efficient and scalable parallel molecular dynamics codes for largescale biomolecular simulations in the open source domain. Namd is a parallel molecular dynamics code designed for highperformance simulation of large biomolecular systems. Namd is a highly scalable parallel molecular dynamics simulator allowing for large scale modeling of cellular systems. Cray and the university of illinois at urbanachampaign. Scalable molecular dynamics for large biomolecular systems. The selfassembly process was initiated from random configurations. Scalable molecular dynamics with namd northwestern scholars. Molecular dynamics programs simulate the behavior of biomolecular systems, leading to understanding of their functions. This study presented proof that there were three major selfassembled arrangements which. Hirasaki and walter g chapman and dilipkumar asthagiri.
Scalable molecular dynamics with namd wiley online library. Scalable molecular dynamics with namd on the summit system abstract. Greater scalability for parallel molecular dynamics. Namd permitted simulation of a protein dna complex en compassing 36,000 atoms,5 one of the largest simulations car ried. 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. Molecular dynamics simulation of large biomolecular systems and long timescale biological phenomena requires tremendous computing power. 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. However, the computational complexity of such simulations is enormous. Phillips and others published scalable molecular dynamics with namd find, read and cite all the research you need on. Phillips and others published scalable molecular dynamics with namd find, read and cite all the research you need on researchgate. Parallel machines provide the potential to meet this computational challenge. With an objectbased hybrid force and spatial decomposition. Oct 12, 2005 namd is a parallel molecular dynamics code designed for high.
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. 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. Pdf scalable molecular dynamics with namd james phillips. Petascale molecular dynamics with namd center for scalable. We have used the roccc compiler toolset to generate the circuit and implemented it on the sgi altix 4700. New structural insights into kir channel gating from. Greater scalability for parallel md 285 must correctly interleave the parallel communication logic. Together with visual molecular dynamics vmd and qwikmd, namds interface provides access to hybrid qmmm simulations in an integrated, comprehensive, customizable, and easytouse suite. 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. The simulations for q23htt were performed using namd phillips et al. Biomolecular reaction and interaction dynamics global. Namd is a parallel molecular dynamics code designed for high.
Amd epyc 7002 series processors and namd molecular. 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. The official namd home page is located at tcbg namd research. Generalized scalable multiple copy algorithms for molecular. 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. It achieves best performance when there is a proper balance between cpu and gpu. 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 scales to hundreds of processors on highend parallel platforms, as well as tens of processors on lowcost commodity clusters, and. This guide includes the capabilities of the program, how to use these capabilities, the necessary input. Scalable molecular dynamics with namd phillips 2005.
They differ in how the force computations are assigned to processors. The molecular dynamics computation involves calculating forces on all atoms during. Namd performance on xeonscalable 8180 and 8 gtx 1080ti gpus. Namd2 handles this problem in part by providing the infrastructure class hierarchy that embodies commonly needed molecular dynamics mechanisms. Theoretical and computational biophysics group tcb. 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. Phillips and others published scalable molecular dynamics with namd. Parts of this infrastructure include generic force compu. Dec 01, 2005 namd is a parallel molecular dynamics code designed for high. Namd uses the popular molecular visualization package vmd for simulation setup and trajectory analysis, but is also filecompatible with amber, charmm, and xplor. 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. Namd works with amber and charmm potential functions, parameters, and file. Namd can be used on any machine from laptop to supercomputers running linuxunix, mac os x, or.
Amd epyc processors bring a new balance to the datacenter. A portable and highly scalable program for biomolecular. 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. 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. Scalable molecular dynamics with namd on the summit system 1. Pdf molecular dynamics simulations of nmr relaxation and. Of these, namd is regarded as the most scalable and the most efficient on highly parallel runs, although gromacs typically achieves superior performance on. Scalable molecular dynamics with namd on blue genel sameer kumar1, chao huang 2, gengbin zheng, eric bohm abhinav bhatele2, james c. This peptide is one of the two peptides to be examined in the md project. The principal investigator is benoit roux from the university of chicago. Of these, namd is regarded as the most scalable and the most efficient on highly parallel runs, although.
The most cited manuscript is this category is scalable molecular dynamics with namd 49, which as observed is a work of computational chemistry. Namd is a parallel, objectoriented molecular dynamics code designed for highperformance simulation of large biomolecular systems. Namd a parallel objectoriented molecular dynamics program pdf. Scalable molecular dynamics with namd europe pmc article. More recent proposals for scalable molecular dynamics 8, 9, 10 use the basic strategy of hybrid decomposition, which originated from namd 2. Namd scales to hundreds of processors on highend parallel platforms, as well as tens of processors on lowcost commodity clusters, and also runs on.
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