Allatomistic molecular mechanics methods have the following properties. Optimized particlemesh ewaldmultipletime step integration for. Namd not another molecular dynamics simulator nmr nuclear magnetic resonance npi native port interface p3me particle particle particle mesh ewald pbc periodic boundary condition pim particle information memory pme particle mesh ewald qmmi imaginary charge mesh memory qmmr real charge mesh memory rsce reciprocal sum compute engine. Lammps, largescale atomicmolecular massively parallel simulator, is a classical molecular dynamics md code created for simulating molecular and atomic systems such as proteins in solution, liquidcrystals, polymers, zeolites, or simple lenardjonesium. Routine microsecond molecular dynamics simulations with amber on gpus.
Routine microsecond molecular dynamics simulations with. This uses the force field to calculate the forces acting on each particle and a suitable integrator to model the dynamics of the particles and predict trajectories. Particle mesh ewald method for threedimensional systems. The particle mesh ewald pme method is used for e cient longrange electrostatic calculations in molecular dynamics md. The parallel implementation of a molecular dynamics code suitable for simulation of general molecular systems using spatialdecomposition methods is discussed. Elbers reaction path method, global optimization via our potential smoothing and search algorithms, molecular dynamics with simulated annealing and stochastic dynamics options, particle mesh ewald summation, monte carlo minimization, atomic multipole treatment of electrostatics with explicit dipole polarizability. Parallelized particle mesh ewald fft and reciprocal space sum.
I am currently using this method to solve for water molecules molecular dynamics simulation. Download citation particle mesh ewald and rrespa for parallel molecular dynamics simulations the parallel implementation of a molecular dynamics code suitable for simulation of general. However, the ewald method has enjoyed widespread use since the 1970s in computer simulations of particle systems, especially those whose particles interact via an inverse square force law such as gravity or electrostatics. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms. In this project, pme is implemented for a single gpu alongside the existing cpu implementation, using the code base of an open source md software gromacs and nvidia cuda toolkit. Longrange coulombic forces are computed using a particle mesh ewald pppm technique.
Jun 24, 2014 long range interactions play a major role in molecular dynamics md simulations, also periodic boundary conditions pbc is used in most simulations to approach bulk systems, which further complicates the calculation. I wrote a tutorial on this topic with an accompanying implementation of the ewald summation and particlemesh ewald methods for dispersive not coulomb potentials that. Our method applies a symmetric trotter factorization of the liouville operator based on the positionverlet scheme to newtonian and langevin dynamics. Tackling exascale software challenges in molecular dynamics. Optimized particlemesh ewaldmultipletime step integration for molecular. Charmmgui input generator can be used for the preparation of genesis input files. The smooth particle mesh ewald summation method is widely used to efficiently compute longrange electrostatic force terms in molecular dynamics simulations, and there has been considerable work. Parallel implementation of the treecode ewald method. Fast forwarding to today, the current amber software suite is divided into two parts. Highlyparallelized particle mesh ewald method pme scalable md simulations for huge systems 100,000,000 atoms trajectory analysis tools rmsd, rmsf, pca, wham, mbar, etc. Numerical integration techniques are also of interest in molecular dynamics. Molecular dynamics texas advanced computing center. We describe an implementation for nvidia graphical processing units gpus which are general purpose computing. Download citation particlemesh ewald and rrespa for parallel molecular dynamics simulations the parallel implementation of a molecular dynamics code suitable for simulation of general.
An implementation of the smooth particle mesh ewald method. Abraham computational proteomics group, john curtin school of medical research, australian national university, po box 334, canberra, act, 2601, australia. Particle mesh pm is a computational method for determining the forces in a system of particles. The method is based on interpolation of the reciprocal space ewald sums and evaluation of the resulting convolutions using fast fourier transforms. In this project, pme is implemented for a single gpu alongside the existing cpu implementation, using the code base of an open source md. Sep 10, 20 routine microsecond molecular dynamics simulations with amber on gpus. Optimization of parameters for molecular dynamics simulation using smooth particle. Journal of chemical theory and computation 20, 9 12, 55995609. Particlemesh ewald and rrespa for parallel molecular dynamics simulations, s. Release binaries contain fftw under special license. An implementation of the smooth particle mesh ewald method on. Timings and accuracies are presented for three large crystalline ionic systems. Stevens, in proc of the eighth siam conference on parallel processing for scientific computing, minneapolis, mn, march 1997. The art of numerical simulation of biomolecular dynam.
Particle mesh ewald pme method ewald summation was developed as a method in theoretical physics, long before the advent of computers. Optimization of parameters for molecular dynamics simulation using smooth particlemesh ewald in gromacs 4. Long range interactions play a major role in molecular dynamics md simulations, also periodic boundary conditions pbc is used in most simulations to approach bulk systems, which further complicates the calculation. A comparison of the spectral ewald and smooth particle mesh. Namd not another molecular dynamics simulator nmr nuclear magnetic resonance npi native port interface p3me particleparticle particlemesh ewald pbc periodic boundary condition pim particle information memory pme particlemesh ewald qmmi imaginary charge mesh memory qmmr real charge mesh memory rsce reciprocal sum compute engine.
Amber18, which is centered around the pmemd simulation program pmemd stands. Molecular dynamics simulations on solvated biomolecular systems. Citeseerx document details isaac councill, lee giles, pradeep teregowda. Computer simulation using particles iop publishing ltd. The potential could be the electrostatic potential among n point charges i.
These particles could be atoms, stars, or fluid components and so the method is applicable to many fields, including molecular dynamics and astrophysics. An efficient particle mesh ewald approach for including. Air force research laboratory dod supercomputing resource center afrl dsrc. The particle mesh ewald method leads to stable trajectories of dna. A comparison of particleparticle, particlemesh and ewald. Effect of periodic box size on aqueous molecular dynamics. Implementation of the particle mesh ewald method on a gpu. The tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. A multipletimescale integration method known as rrespa is.
Optimization of parameters for molecular dynamics simulation using. Optimized particlemesh ewaldmultipletime step integration. Given enough sampling and subject to the ergodic hypothesis, molecular dynamics trajectories can be used to estimate thermodynamic. Intel parallel computing center at rwth aachen university intel software jump to navigation. In many cases, molecular dynamics is applied to simulations on molecules with a very large number of atoms as well, e. Optimized particlemesh ewaldomultipletime step integration for.
Tinker has the ability to use any of several common parameter sets, such as amber ff94, ff96, ff98, ff99, ff99sb, charmm 19, 22, 22cmap, allinger mm. Mdgrape4 is designed to achieve strong scalability for protein md simulations through the integration of generalpurpose cores, dedicated pipelines, memory banks and network interfaces nifs to create a system on chip soc. Optimization of parameters for molecular dynamics simulation. Extension of the amber molecular dynamics software to. Much faster minimizer based on conjugate gradient method. Gpu technology conference 2010 sessions on molecular. Improved load balancer with scaling to over 1024 processors. Molecular dynamics simulations accelerated by gpu for biological macromolecules with a nonewald scheme for electrostatic interactions. Ambertools18, a collection of freely available programs for biomolecular simulation and analysis. Aug 06, 2014 we are developing the mdgrape4, a specialpurpose computer system for molecular dynamics md simulations. Ewald summation, named after paul peter ewald, is a method for computing longrange interactions e.
Salomonferrer r1, gotz aw1, poole d2, le grand s2, walker rc. Lammps is a classical molecular dynamics code designed for simulating molecular and atomic systems on parallel computers using spatialdecomposition techniques. Abstract we develop an efficient multiple time step mts force splitting scheme for biological applications in the amber program in the context of the particle mesh ewald pme algorithm. The force on the atoms is the negative gradient of the charmm potential energy 14. Particle mesh ewald method for threedimensional systems with. Case,b and tamar schlicka,c department of chemistry and courant institute of mathematical sciences, new york university and the. The framework supports the charmm 19 and 28a2 force fields and is able to process pdb, psf, xyz and dcd trajectory files. Explicit solvent particle mesh ewald romelia salomonferrer, andreas w. While several adaptations of generalized born have attained excellent speedup on gpus, high performance particle mesh ewald has been more elusive. Genesis generalizedensemble simulation system is molecular dynamics and modeling software for bimolecular systems such as proteins, lipids, glycans, and their complexes. The method is most often applied to condensed phase v. London 362 2004 1835, making use of a novel 3d fast fourier. The main use of molecular mechanics is in the field of molecular dynamics. These methods have been successfully employed in the past decades at varied levels of molecular simulations, but the related physical parameters should be carefully.
A particle mesh ewald method for calculating coulomb interactions in threedimensional 3d systems with twodimensional 2d periodicity was developed. An efficient particle mesh ewald approach for including longrange electrostatics in qmmm molecular dynamics simulations ross c. A 3d convolution engine for computing the reciprocalspace. In the most common version, the trajectories of atoms and molecules are determined by numerically solving newtons equations of motion for a system. It runs on any parallel platform that supports f90 and the mpi messagepassing library or on singleprocessor workstations. Optimized particlemesh ewaldomultipletime step integration for molecular. We are developing the mdgrape4, a specialpurpose computer system for molecular dynamics md simulations. An efficient particle mesh ewald approach for including long. A highly optimized implementation of this method is available in gromacs, a widely used software for molecular dynamics simulations.
E optimization of parameters for molecular dynamics simulation using smooth particlemesh ewald in gromacs 4. Calkins department of chemistry, university of rochester, summer 2006 ret program. The calculation was run in explicit solvent using periodic boundaries and the particle mesh ewald method of treating long range electrostatics. Protomol is an objectoriented, component based, framework for molecular dynamics md simulations. Lammps, largescale atomic molecular massively parallel simulator, is a classical molecular dynamics md code created for simulating molecular and atomic systems such as proteins in solution, liquidcrystals, polymers, zeolites, or simple lenardjonesium. Gpu technology conference 2010 sessions on molecular dynamics. Routine microsecond molecular dynamics simulations with amber. This computational cost can be reduced by employing electrostatics methods such as particle mesh ewald onlogn or good spherical cutoff techniques on. In this paper, we discuss an efficient parallel implementation of the treecode ewald method for fast evaluation of longrange coulomb interactions in a periodic system for molecular dynamics simulations. In molecular dynamics md simulations with periodic boundary conditions, the energy of the electrostatic interactions is often computed using the particle mesh ewald pme summation, which requires the system to be electrically neutral. Extension of the amber molecular dynamics software to intels. Longrange coulombic forces are computed using a particlemesh ewald pppm technique. Even when that is not the case, adding ions is commonly used to make the net electric charge of the system zero.
Performance characterization of a molecular dynamics code. Md trajectories obtained by genesis can be visualized with vmd and other software. Computational proteomics group, john curtin school of medical research, australian national university, po box 334, canberra, act, 2601, australia. The ewald sum method reduces computation by splitting any longrange force into a shortrange force done via particle particle calculations and a smoothly varying force which is approximated by particle mesh calculations. Abstract the particle mesh ewald pme method is used for ecient long range electrostatic calculations in molecular dynamics md. Optimized particlemesh ewaldmultipletime for molecular dynamics.
The method is most often applied to condensed phase. Computational efficiency and accuracy of this method were evaluated for a tip3p water system with 2928 particles in a cubic box with 2d periodicity. Since the accuracies of the zmm have been revealed to be sufficient in previous studies, it is highly desirable to clarify its practical performance. It was first developed as the method for calculating electrostatic energies of ionic crystals, and is now commonly used for calculating longrange interactions in computational chemistry. Tutorial b1 section 1 the amber molecular dynamics package. Tackling exascale software challenges in molecular. The parallelization is based on an adaptive decomposition scheme.
Walker, title routine microsecond molecular dynamics simulations with amber part ii. What is ewald summation, and why is the particle mesh ewald. Abstract we develop an efficient multiple time step mts force splitting scheme for biological applications in the amber program in the context of the particlemesh ewald pme algorithm. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic evolution of the system. For this reason the hybrid system is known as the particle particle particle mesh ewald method. Particle mesh ewald and rrespa for parallel molecular dynamics simulations, s. It is designed for high flexibility, easy extendibility and maintenance, and high performance demands, including. We present an implementation of explicit solvent particle mesh ewald pme classical molecular dynamics md within the pmemd molecular dynamics engine, that forms part of the amber v14 md software package, that makes use of intel xeon phi coprocessors by offloading portions of the pme direct summation and neighbor list build to the coprocessor. In this paper, the performance of the zmm is compared with that of the smooth particle mesh ewald method spme, where the both methods are implemented in molecular dynamics software package gromacs. Particleparticleparticlemesh p3m is a fourierbased ewald summation method to calculate potentials in nbody simulations. The average structure from a 1 nanosecond molecular dynamics simulation of a 10 base pair polyapoltt dna duplex.
Molecular dynamics is a highly computeintensive simulation tool for determining the thermodynamic. Stevens, particlemesh ewald and rrespa for parallel molecular dynamics simulations, in proc of the eighth siam conference on parallel processing for scientific computing, minneapolis, mn, march 1997. What is ewald summation, and why is the particle mesh. Tackling exascale software challenges in molecular dynamics simulations with gromacs. The smooth particle mesh ewald summation method is widely used to efficiently compute longrange electrostatic force terms in molecular dynamics simulations, and there has been considerable work in developing optimized implementations for a variety of parallel computer architectures. Molecular dynamics md is a computer simulation method for analyzing the physical movements of atoms and molecules. Genesis is open source software distributed under the gplv2 license.
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