A molecular dynamics method for simulations in the canonical ensemble
TL;DR: In this paper, a molecular dynamics simulation method which can generate configurations belonging to the canonical (T, V, N) ensemble or the constant temperature constant pressure ensemble was proposed, which is tested for an atomic fluid (Ar) and works well.
Abstract: A molecular dynamics simulation method which can generate configurations belonging to the canonical (T, V, N) ensemble or the constant temperature constant pressure (T, P, N) ensemble, is proposed. The physical system of interest consists of N particles (f degrees of freedom), to which an external, macroscopic variable and its conjugate momentum are added. This device allows the total energy of the physical system to fluctuate. The equilibrium distribution of the energy coincides with the canonical distribution both in momentum and in coordinate space. The method is tested for an atomic fluid (Ar) and works well.
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TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
Abstract: This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.
13,116 citations
TL;DR: An extension of the CHARMM force field to drug‐like molecules is presented, making it possible to perform “all‐CHARMM” simulations on drug‐target interactions thereby extending the utility ofCHARMM force fields to medicinally relevant systems.
Abstract: The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to drug-like molecules is presented. The resulting CHARMM General Force Field (CGenFF) covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds. The parametrization philosophy behind the force field focuses on quality at the expense of transferability, with the implementation concentrating on an extensible force field. Statistics related to the quality of the parametrization with a focus on experimental validation are presented. Additionally, the parametrization procedure, described fully in the present article in the context of the model systems, pyrrolidine, and 3-phenoxymethylpyrrolidine will allow users to readily extend the force field to chemical groups that are not explicitly covered in the force field as well as add functional groups to and link together molecules already available in the force field. CGenFF thus makes it possible to perform "all-CHARMM" simulations on drug-target interactions thereby extending the utility of CHARMM force fields to medicinally relevant systems.
4,553 citations
TL;DR: The results indicate that the revised CHARMM 36 parameters represent an improved model for the modeling and simulation studies of proteins, including studies of protein folding, assembly and functionally relevant conformational changes.
Abstract: While the quality of the current CHARMM22/CMAP additive force field for proteins has been demonstrated in a large number of applications, limitations in the model with respect to the equilibrium between the sampling of helical and extended conformations in folding simulations have been noted. To overcome this, as well as make other improvements in the model, we present a combination of refinements that should result in enhanced accuracy in simulations of proteins. The common (non Gly, Pro) backbone CMAP potential has been refined against experimental solution NMR data for weakly structured peptides, resulting in a rebalancing of the energies of the α-helix and extended regions of the Ramachandran map, correcting the α-helical bias of CHARMM22/CMAP. The Gly and Pro CMAPs have been refitted to more accurate quantum-mechanical energy surfaces. Side-chain torsion parameters have been optimized by fitting to backbone-dependent quantum-mechanical energy surfaces, followed by additional empirical optimization targeting NMR scalar couplings for unfolded proteins. A comprehensive validation of the revised force field was then performed against data not used to guide parametrization: (i) comparison of simulations of eight proteins in their crystal environments with crystal structures; (ii) comparison with backbone scalar couplings for weakly structured peptides; (iii) comparison with NMR residual dipolar couplings and scalar couplings for both backbone and side-chains in folded proteins; (iv) equilibrium folding of mini-proteins. The results indicate that the revised CHARMM 36 parameters represent an improved model for the modeling and simulation studies of proteins, including studies of protein folding, assembly and functionally relevant conformational changes.
3,421 citations
TL;DR: It is shown how the new RESPA methods are related to predictor–corrector integrators and how these methods can be used to accelerate the integration of the equations of motion of systems with Nose thermostats.
Abstract: The Trotter factorization of the Liouville propagator is used to generate new reversible molecular dynamics integrators This strategy is applied to derive reversible reference system propagator algorithms (RESPA) that greatly accelerate simulations of systems with a separation of time scales or with long range forces The new algorithms have all of the advantages of previous RESPA integrators but are reversible, and more stable than those methods These methods are applied to a set of paradigmatic systems and are shown to be superior to earlier methods It is shown how the new RESPA methods are related to predictor–corrector integrators Finally, we show how these methods can be used to accelerate the integration of the equations of motion of systems with Nose thermostats
3,155 citations
TL;DR: An unusually high value, lambda approximately 6600 W/m K, is suggested for an isolated (10,10) nanotube at room temperature, comparable to the thermal conductivity of a hypothetical isolated graphene monolayer or diamond.
Abstract: Recently discovered carbon nanotubes have exhibited many unique material properties including very high thermal conductivity. Strong sp 2 bonding configurations in carbon network and nearly perfect self-supporting atomic structure in nanotubes give unusually high phonon-dominated thermal conductivity along the tube axis, possibly even surpassing that of other carbon-based materials such as diamond and graphite (in plane). In this chapter, we explore theoretical and experimental investigations for the thermal-transport properties of these materials.
3,011 citations
Cites methods from "A molecular dynamics method for sim..."
...In this approach, the temperature T of the sample is regulated by a Nosé-Hoover thermostat [28], [29], which indicates the temperature of a surrounding thermal reservoir....
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References
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TL;DR: In this paper, a new Lagrangian formulation is introduced to make molecular dynamics (MD) calculations on systems under the most general externally applied, conditions of stress, which is well suited to the study of structural transformations in solids under external stress and at finite temperature.
Abstract: A new Lagrangian formulation is introduced. It can be used to make molecular dynamics (MD) calculations on systems under the most general, externally applied, conditions of stress. In this formulation the MD cell shape and size can change according to dynamical equations given by this Lagrangian. This new MD technique is well suited to the study of structural transformations in solids under external stress and at finite temperature. As an example of the use of this technique we show how a single crystal of Ni behaves under uniform uniaxial compressive and tensile loads. This work confirms some of the results of static (i.e., zero temperature) calculations reported in the literature. We also show that some results regarding the stress‐strain relation obtained by static calculations are invalid at finite temperature. We find that, under compressive loading, our model of Ni shows a bifurcation in its stress‐strain relation; this bifurcation provides a link in configuration space between cubic and hexagonal close packing. It is suggested that such a transformation could perhaps be observed experimentally under extreme conditions of shock.
13,937 citations
TL;DR: In this paper, it is shown that time averages of properties of the simulated fluid are equal to averages over the isoenthalpic-isobaric, canonical, and isothermal-isboric ensembles.
Abstract: In the molecular dynamics simulation method for fluids, the equations of motion for a collection of particles in a fixed volume are solved numerically. The energy, volume, and number of particles are constant for a particular simulation, and it is assumed that time averages of properties of the simulated fluid are equal to microcanonical ensemble averages of the same properties. In some situations, it is desirable to perform simulations of a fluid for particular values of temperature and/or pressure or under conditions in which the energy and volume of the fluid can fluctuate. This paper proposes and discusses three methods for performing molecular dynamics simulations under conditions of constant temperature and/or pressure, rather than constant energy and volume. For these three methods, it is shown that time averages of properties of the simulated fluid are equal to averages over the isoenthalpic–isobaric, canonical, and isothermal–isobaric ensembles. Each method is a way of describing the dynamics of a certain number of particles in a volume element of a fluid while taking into account the influence of surrounding particles in changing the energy and/or density of the simulated volume element. The influence of the surroundings is taken into account without introducing unwanted surface effects. Examples of situations where these methods may be useful are discussed.
4,998 citations
TL;DR: In this paper, it was shown that different pair potentials lead to different crystal structures, with the use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell.
Abstract: With use of a Lagrangian which allows for the variation of the shape and size of the periodically repeating molecular-dynamics cell, it is shown that different pair potentials lead to different crystal structures.
2,630 citations
TL;DR: The constant pressure molecular dynamics (MD) method proposed by Andersen and extended by Parrinello and Rahman to allow changes in the shape of the MD cell is discussed in this paper.
Abstract: Technical aspects of the constant pressure molecular dynamics (MD) method proposed by Andersen and extended by Parrinello and Rahman to allow changes in the shape of the MD cell are discussed. The new MD method is extended to treat molecular systems and to include long range charge-charge interactions. Results on the conservation laws, the frequency of oscillation of the MD cell, and the equations which constrain the shape of the MD cell are also given. An additional constraint is introduced to stop the superfluous MD cell rotation which would otherwise complicate the analysis of crystal structures. The method is illustrated by examining the behaviour of solid nitrogen at high pressure.
2,562 citations
TL;DR: In this article, the molecular dynamics algorithm of Verlet was extended to study dense neutral assemblies of charged particles under specified V-T conditions, and the results were obtained for liquid alkali chlorides at 1273°K.
472 citations