On the relative merits of flexible versus rigid models for use in computer simulations of molecular liquids

Tironi, Ilario G.; Brunne, Roger M.; Gunsteren, Wilfred F. van

doi:10.1016/0009-2614(95)01434-9

Cited by 87 publications

(93 citation statements)

References 28 publications

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“…There are several possible reasons for this improved agreement. For example, it is possible that the rigid water approximation mimics some of the effects coming from the quantum nature of protons, which are explicitly ignored in simulations that allow for intramolecular flexibility with classical dynamics 30,32,33 . More specifically, in Ref.…”

Section: Resultsmentioning

confidence: 99%

“…More specifically, in Ref. 32 it was pointed out that at a temperature of 300 K, k B T ∼ 200 cm −1 , whereas the high frequency intramolecular modes in water range from ∼1000 to 3500 cm −1 . In the quantum system the amount of thermal energy available to excite vibrational modes is much smaller than the lowest possible intramolecular vibrational excitations,h…”

Section: Resultsmentioning

confidence: 99%

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A first principles simulation of rigid water

Allesch

Schwegler

Gygi

et al. 2004

The Journal of Chemical Physics

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We present the results of Car-Parrinello (CP) simulations of water at ambient conditions and under pressure, using a rigid molecule approximation. Throughout our calculations, water molecules were maintained at a fixed intramolecular geometry corresponding to the average structure obtained in fully unconstrained simulations. This allows us to use larger time steps than those adopted in ordinary CP simulations of water, and thus to access longer time scales. In the absence of chemical reactions or dissociation effects, these calculations open the way to ab initio simulations of aqueous solutions that require timescales substantially longer than presently feasible (e.g. simulations of hydrophobic solvation). Our results show that structural properties and diffusion coefficients obtained with a rigid model are in better agreement with experiment than those determined with fully flexible simulations. Possible reasons responsible for this improved agreement are discussed.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

A first principles simulation of rigid water

Allesch

Schwegler

Gygi

et al. 2004

The Journal of Chemical Physics

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“…It has been argued that flexible water models are not superior to their rigid counterparts because of the inherent quantum nature of stretching and bending vibrations. 49 However, intramolecular flexibility is clearly important in the modeling of larger molecules with additional conformational options. Thus, it seems consistent to retain the same intramolecular degrees of freedom in a solvent model to be used in solvating larger species.…”

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confidence: 99%

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

Ren¹,

2003

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A new classical empirical potential is proposed for water. The model uses a polarizable atomic multipole description of electrostatic interactions. Multipoles through the quadrupole are assigned to each atomic center based on a distributed multipole analysis (DMA) derived from large basis set molecular orbital calculations on the water monomer. Polarization is treated via self-consistent induced atomic dipoles. A modified version of Thole's interaction model is used to damp induction at short range. Repulsion-dispersion (vdW) effects are computed from a buffered 14-7 potential. In a departure from most current water potentials, we find that significant vdW parameters are necessary on hydrogen as well as oxygen. The new potential is fully flexible and has been tested versus a variety of experimental data and quantum calculations for small clusters, liquid water, and ice. Overall, excellent agreement with experimental and high level ab initio results is obtained for numerous properties, including cluster structures and energetics and bulk thermodynamic and structural measures. The parametrization scheme described here is easily extended to other molecular systems, and the resulting water potential should provide a useful explicit solvent model for organic solutes and biopolymer modeling. IntroductionEmpirical potential energy functions derived from classical molecular mechanics are central to computational modeling at the atomic level. Molecular mechanics has long enjoyed great success in application to many classes of isolated, gas-phase organic compounds. 1 Beginning with the pioneering work of Bernal and Fowler, 2 water has probably been the target of more potential energy models than any other substance. An interesting overview and historical perspective on the development of water models was recently presented by Finney. 3 Simple nonpolarizable pairwise-additive models that describe the average structure and energetics of liquid water have been in wide use for many years (e.g., TIP3P 4 and SPC 5 ). The recently developed TIP5P potential exhibits excellent agreement with the experimental internal energy, density, and O‚‚‚O radial distribution at room temperature. 6 These models typically use fixed atom-based partial charges to model electrostatics and include polarization response to the environment only in an averaged, mean-field sense. As a result, nonpolarizable potentials that provide excellent descriptions of the homogeneous bulk phase are poor models for gas phase clusters and for nonpolar solutes in polar solvents. For example, the gas phase binding energy of the water dimer is overestimated by more than 30% in the TIP5P model. In application to large biomolecular systems, there is concern that such models cannot correctly account for situations where the same nonpolarizable moiety is exposed to different electrostatic environments, either within a single large static structure or during a course of simulation. In addition, there is an inherent inconsistency in most nonpolarizable models related to thei...

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“…However, we (and many others [76,58,85,64,67,59,41,86,87,71,69,88,89,90,77,69,91,50]) have preferred to use the classical unconstrained model as a reference to be able to assess the influence of the imposition of constraints in an incremental way consisting of a series of controlled steps. Although some works have advocated the point of view that the proper justification of constrained models should come from a quantum mechanical treatment [49,54,72,92,56,43,79,83,93,94], and the comparison to experiment [94] or to quantum mechanics is indeed more relevant in terms of the absolute accuracy of the constrained models, the approximations connecting the former to the latter are many, thus obscuring the influence of each individual step. In particular, it is worth mentioning refs.…”

Section: Flexible Vs Hard Constraintsmentioning

confidence: 99%

The canonical equilibrium of constrained molecular models

Echenique

Cavasotto

García-Risueño

2011

Eur. Phys. J. Spec. Top.

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Abstract. In order to increase the efficiency of the computer simulation of biological molecules, it is very common to impose holonomic constraints on the fastest degrees of freedom; normally bond lengths, but also possibly bond angles. Since the maximum time step required for the stability of the dynamics is proportional to the shortest period associated with the motions of the system, constraining the fastest vibrations allows to increase it and, assuming that the added numerical cost is not too high, also increase the overall efficiency of the simulation. However, as any other element that affects the physical model, the imposition of constraints must be assessed from the point of view of accuracy: both the dynamics and the equilibrium statistical mechanics are model-dependent, and they will be changed if constraints are used. In this review, we investigate the accuracy of constrained models at the level of the equilibrium statistical mechanics distributions produced by the different dynamics. We carefully derive the canonical equilibrium distributions of both the constrained and unconstrained dynamics, comparing the two of them by means of a "stiff" approximation to the latter. We do so both in the case of flexible and hard constraints, i.e., when the value of the constrained coordinates depends on the conformation and when it is a constant number. We obtain the different correcting terms associated with the kinetic energy mass-metric tensor determinants, but also with the details of the potential energy in the vicinity of the constrained subspace (encoded in its first and second derivatives). This allows us to directly compare, at the conformational level, how the imposition of constraints changes the thermal equilibrium of molecular systems with respect to the unconstrained case. We also provide an extensive review of the relevant literature, and we show that all models previously reported can be considered special cases of the most general treatments presented in this work. Finally, we numerically analyze a simple methanol molecule in order to illustrate the theoretical concepts in a practical case.

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On the relative merits of flexible versus rigid models for use in computer simulations of molecular liquids

Cited by 87 publications

References 28 publications

A first principles simulation of rigid water

A first principles simulation of rigid water

Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation

The canonical equilibrium of constrained molecular models

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