Possible artifacts due to the use of ewald summation in molecular dynamics simulations will be discussed, and finally the treatment of free energy perturbation, in particular the free energy of charging an ion in water, will be discussed in the context of ewald summation. 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 you may find helpful. Tinker has the ability to use any of several common parameter sets, such as amber ff94, ff96, ff98, ff99, charmm 19, 22 and 22cmap, allinger mm mm21991 and mm32000, opls oplsua, oplsaa and oplsaal, as well as our amoeba. I am currently using this method to solve for water molecules molecular dynamics simulation. 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. Ewald summation for coulomb interactions in a periodic. Quantifying artifacts in ewald simulations of inhomogeneous. Molecular dynamics simulations aim at solving the equations of motion of the atoms belonging to a molecular system using explicit time propagation and taking into account the effect of temperature on the atomic velocities as opposite to geometry optimization. Extension of the amber molecular dynamics software to. Doublestranded dna is highly charged and polar, with phosphate groups in its backbone and their counterions, and thus precise treatment for the. Molecular dynamics of mixtures mdynamix is a computer software package for general purpose molecular dynamics to simulate mixtures of molecules, interacting by amber and charmmlike force fields in periodic boundary conditions. Focus is also given to methods for accelerating ewald summation in monte carlo simulations. Performance evaluation of the zeromultipole summation method in modern molecular dynamics software. Finally, we comment on the cpu time required to calculate the ewald sum eq.
A pointer array p indicates where in the neighbor list array l the. Because of a careful equilibration protocol and the use of the ewald summation in calculating the electrostatic interactions, the rna structure. For nonneutral systems, the ewald algorithm implicitly introduces a uniform background charge distribution that effectively neutralizes the simulation box. Thus, ewalds idea is to replace a single divergent summation with two convergent summations. The electrostatic energy of a periodic system can be expressed by a lattice sum over all pair. Thanks to victor munoz robles and jeandidier marechal. Namd is another md simulations engine, which is well optimized and run also in windows systems, without the need for the cygwin. Ewald summation for molecular simulations acs publications. The method of molecular dynamics coupled with the application of periodic boundary conditions pbcs allows larger systems to be modelled at reduced computing costs. It is designed for high flexibility, easy extendibility and maintenance, and high performance demands, including. Enuf has a behavior very similar to ewald summation and can be easily and efficiently implemented in existing simulation programs. Molecular dynamics investigations of hammerhead ribozyme. 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.
Note that the u coulomb contribution from longrange columbic interactions is handled differently using an ewald summation and is described separately in the next section. A 3d convolution engine for computing the reciprocalspace. In this article, expressions are provided for implementing ewald summation for any inverse power potential in a range of different simulations. Ewald summation is an important technique for molecular simulation. For this purpose, the formula for potential and force i have used is. Molecular dynamics md is a computer simulation of physical movements of atoms and molecules. Levy department of chemisoy, rutgers university, new brunswick, nj 08903, usa received 29 november 1990. Study of temperature dependence of thermal conductivity in. Tinker has the ability to use any of several common parameter sets, such as amber ff94, ff96, ff98, ff99, charmm 19, 22 and 22cmap, allinger mm mm21991 and mm32000, opls oplsua, oplsaa and oplsaal, as well as our amoeba polarizable atomic multipole force field. The sensitivity of the orientational structure of water in the. We found that ex plicit evaluation of the ewald sum increases the cpu time by about 1. Molecular dynamics md is a form of computer simulation wherein atoms and molecules are allowed to interact for a period of time under known laws of physics, giving a view of the motion of the atoms.
The framework supports the charmm 19 and 28a2 force fields and is able to process pdb, psf, xyz and dcd trajectory files. Pressure calculation in polar and charged systems using ewald. Calculation of longrange forces in molecular dynamics. Ewald summation for coulomb interactions in a periodic supercell.
The following 36 pages are in this category, out of 36 total. This category contains pages about software used for molecular dynamics simulations. For brevity, ewald summation and ewald sum will be used interchangeably. Ewald summation in the molecular dynamics simulation of large.
The code implements the latest stateoftheart algorithms for molecular dynamics and monte carlo mc in various ensembles including symplecticmeasurepreserving integrators, ewald summation, configurationalbias mc, continuous fractional component mc, reactive. Computer simulations of dipolar fluids using ewald. 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. Ewald summation for molecular simulations journal of. Molecular dynamics md is a computer simulation method for analyzing the physical movements of atoms and molecules. Amber parameters are used for standard residues, and ambers antechamber module also included with chimera is used to assign parameters to nonstandard residues. Ive only ever used the ewald sum, ive never implemented it myself. A new software package, raspa, for simulating adsorption and diffusion of molecules in flexible nanoporous materials is presented. Ewald summation for molecular simulations journal of chemical. Physics stack exchange is a question and answer site for active researchers, academics and students of physics. Introduction ewald summation was introduced in 1921 23 as a technique to sum the longrange interactions between particles and all their infinite periodic images efficiently. Snurrd3 avan t hoff institute of molecular sciences, university of amsterdam, science park 904, 1098xh amsterdam, the netherlands.
Because a uniform distribution of counter charges typically. Ewald summation and multiple time step methods for. A complete package for molecular mechanics, dynamics and modeling of molecules, especially biomacromolecules. Molecular dynamics md simulations of a doublestranded dna with explicit water and small ions were performed with the zerodipole summation zd method, which was recently developed as one of the non ewald methods.
In this article, expressions are provided for implementing ewald summation for any inverse power potential in a range of. Molecular dynamics simulations using fast ewald summation. This presentation will first outline the mathematical development of ewald summation, discussing what is currently understood about the longrange boundary effects, and about the. Ewald summation in the molecular dynamics simulation of. The results are compared with those from molecular dynamics simulations of water using the reaction field method. Molecular simulation via molecular dynamics md or montecarlo. The tinker molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. Aug 06, 2014 we are developing the mdgrape4, a specialpurpose computer system for molecular dynamics md simulations. A typical timestep is one femtosecond 10 15 second. This list may not reflect recent changes learn more. Molecular dynamics simulation is an interface to minimization and molecular dynamics routines provided by mmtk, which is included with chimera. Explicit solvent particle mesh ewald romelia salomonferrer, andreas w. Molecular dynamics simulations of doublestranded dna in.
Computer simulations of dipolar fluids using ewald summations. 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. Cp2k can perform atomistic and molecular simulations of solid state, liquid and biological systems. Application of molecular dynamics in the study of biomolecular phenomena. Molecular dynamics simulations of water with ewald summation for. The code implements the latest stateoftheart algorithms for molecular dynamics and monte carlo in various ensembles including symplecticmeasurepreserving integrators, ewald summation, configurationalbias monte carlo. The code implements the latest stateoftheart algorithms for molecular dynamics and monte carlo mc in various ensembles including symplecticmeasurepreserving integrators, ewald summation, configurationalbias mc, continuous fractional. Because molecular systems generally consist of a vast number of particles, it is impossible to find the properties of such complex systems. Multilevel summation with bspline interpolation for pairwise. 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. Routine microsecond molecular dynamics simulations with amber on gpus.
In the most common version, the trajectories of molecules and atoms are determined by numerically solving the newtons equations of motion for a system of. Newest moleculardynamics questions computational science. Journal of computational chemistry 2018, 39 20, 15511560. Molecular dynamics simulations of water with ewald summation for the long. In the periodic system, the ewald method ewald 1921 has been used as the standard. Calculation of longrange forces in molecular dynamics ewald summation. Because molecular systems generally consist of a vast number of particles, it is impossible to find the properties of such complex systems analytically. Published 24 january 2014 2014 iop publishing ltd modelling and simulation in materials science and engineering, volume 22, number 2.
Introduction to molecular dynamics simulation figure 6. The code implements the latest stateoftheart algorithms for molecular dynamics and monte carlo in various ensembles including symplecticmeasurepreserving integrators, ewald summation, configurationalbias monte carlo, continuous fractional component monte carlo, reactive monte carlo, and bakers minimization. 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. Molecular dynamics investigations of hammerhead ribozyme rna. In molecular dynamics md simulations with periodic boundary conditions, the energy of the electrostatic interactions is often computed using the particlemesh ewald pme summation, which requires the system to be electrically neutral. The derivation here re ects the our thoughts when trying to understand and \internalize the method. Comprehensive life science modeling and simulation suite of applications focused on optimizing drug discovery process. Doublestranded dna is highly charged and polar, with phosphate groups in its backbone and their counterions, and thus precise treatment for the longrange electrostatic. What is ewald summation, and why is the particle mesh ewald. Methods by which to determine conditions for a molecular dynamics md simulation of biological molecules were investigated.
The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic evolution of the system. Routine microsecond molecular dynamics simulations with. The simulation of biologically active molecules poses its own unique set of. I am trying to write a code to calculate the potential and forces, for the same using ewald summation. Even when that is not the case, adding ions is commonly used to make the net electric charge of the system zero. Thus the calculation of the electrostatic energy would be evaluated using. Molecular dynamics simulations of water with ewald summation. Molecular dynamics simulations of water with ewald. We are developing the mdgrape4, a specialpurpose computer system for molecular dynamics md simulations. What is ewald summation, and why is the particle mesh. Longrange electrostatic effects, author sagui, c and darden, t a, abstractnote current computer simulations of biomolecules typically make use of classical molecular dynamics methods, as a very large number tens to hundreds of thousands of atoms are involved over timescales of. It is a free software, you will just need to register to get it.
Algorithms are included for nve, nvt, npt, anisotropic npt ensembles, and ewald summation to treat electrostatic interactions. The accuracy and efficiency of the direct ewald summation are discussed in terms of the size of a molecular dynamics md ionic system and the ranges of the rspace and qspace summations. Molecular dynamics simulations of water with ewald summation for the long range electrostatic interactions mahfoud belhadj, howard e. Algorithms for molecular dynamics simulations diva portal. Protomol is an objectoriented, component based, framework for molecular dynamics md simulations. The calculations performed in molecular dynamics break down into two main categories, bonded forces and nonbonded forces. Molecular dynamics is much required analysis and it provides an edge to the computational biologist or chemist. Molecular modelling computational chemistry molecular mechanics molecular mechanics force field energy minimization newtons method gradient descent conjugate gradient method ewald summation molecular dynamics langevin dynamics free energy perturbation thermodynamic integration simulated annealing comparison of software for molecular mechanics. The ewald summation method 112 offers a theoretically rigorous approach to the evaluation of electrostatic interactions in. Focus is also given to methods for accelerating ewald summation in. The ewald summation in molecular dynamics simulation. In the periodic system, the ewald method ewald 1921 has been used as. Ewald summation and physically equivalent methods such as particlemesh.
Routine microsecond molecular dynamics simulations with amber. Reciprocalspace ewald electrostatic energy in molecular dynamics simulations arun patel master of applied science, 2007 graduate department of electrical and computer engineering university of toronto abstract many attempts have been made to improve the performance of molecular dynamics. Molecular dynamics can now be routinely applied in the investigation of a wide range of dynamic properties and processes by researchers in numerous fields, including structural biochemistry, biophysics, enzymology, molecular biology, pharmaceutical chemistry, and biotechnology. Molecular dynamics simulations of doublestranded dna in an. Abstract the accuracy and efficiency of the direct ewald summation are discussed in terms of the size of a molecular dynamics md ionic system and the. Molecular dynamics md simulations of a doublestranded dna with explicit water and small ions were performed with the zerodipole summation zd method, which was recently developed as one of the nonewald methods. Study of temperature dependence of thermal conductivity in crosslinked epoxies using molecular dynamics simulations with long range interactions. In perio dic boundary c ondition central simulation cell is replicated in all direction to form an in. Recently, a number of groups have discovered that the use of ewald summation leads to greatly improved stability in molecular dynamics simulations of nucleic acids, proteins and membrane bilayers. The atoms and molecules are allowed to interact for a period of time, giving a view of the motion of the atoms. In particular, we discuss the ewald summation methods, the fast particle mesh. This is a list of computer programs that are predominantly used for molecular mechanics calculations. Basis of molecular dynamics the main algorithm in molecular dynamics simulations is the calculation and summation of all forces between all atoms at each timestep.
Computer simulation of liquids, clarendon press, oxford 1987. Pdf molecular dynamics simulations of biomolecules. Comparison of software for molecular mechanics modeling. Multilevel summation with bspline interpolation for. A alternative derivation of ewald summation 8 b twodimensional ewald summation 9 c onedimensional ewald summation 11 this document gives a simple and selfcontained description of the classical ewald method 1, 2. Ewald summation and multiple time step methods for molecular. Since the accuracies of the zmm have been revealed to be sufficient in previous studies, it is highly desirable to clarify its practical performance. Raspa is a software package for simulating adsorption and diffusion of molecules in flexible nanoporous materials. The ewald summation method charmm v35b1 documentation. Energies, forces, stresses, and hessian elements as well as truncation errors are considered. Ewald summation, named after paul peter ewald, is a method for computing longrange interactions e. An e cient use is made of these in the implementation of the ewald summation when dealing with long range interactions, which can easily be adapted to allow its application to a. In this article, expressions are provided for implementing ewald.
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