Molecular dynamics simulation validation

Small metal clusters are also of interest because of their importance in catalysis. Despite the fact that small clusters should consist of mostly surface atoms, measurement of the photon ionization threshold for Hg clusters suggest that a transition from van der Waals to metallic properties occurs in the range of 20-70 atoms per cluster [88] and near-bulk magnetic properties are expected for Ni, Pd, and Pt clusters of only 13 atoms [89] Theoretical calculations on Sin and other semiconductors predict that the stmcture reflects the bulk lattice for 1000 atoms but the bulk electronic wave functions are not obtained [90]. Bartell and co-workers [91] study beams of molecular clusters with electron dirfraction and molecular dynamics simulations and find new phases not observed in the bulk. Bulk models appear to be valid for their clusters of several thousand atoms (see Section IX-3). 

Bartell and co-workers have made significant progress by combining electron diffraction studies from beams of molecular clusters with molecular dynamics simulations [14, 51, 52]. Due to their small volumes, deep supercoolings can be attained in cluster beams however, the temperature is not easily controlled. The rapid nucleation that ensues can produce new phases not observed in the bulk [14]. Despite the concern about the appropriateness of the classic model for small clusters, its application appears to be valid in several cases [51]. 

The concentration of salt in physiological systems is on the order of 150 mM, which corresponds to approximately 350 water molecules for each cation-anion pair. Eor this reason, investigations of salt effects in biological systems using detailed atomic models and molecular dynamic simulations become rapidly prohibitive, and mean-field treatments based on continuum electrostatics are advantageous. Such approximations, which were pioneered by Debye and Huckel [11], are valid at moderately low ionic concentration when core-core interactions between the mobile ions can be neglected. Briefly, the spatial density throughout the solvent is assumed to depend only on the local electrostatic poten-... 

In literature, some researchers regarded that the continuum mechanic ceases to be valid to describe the lubrication behavior when clearance decreases down to such a limit. Reasons cited for the inadequacy of continuum methods applied to the lubrication confined between two solid walls in relative motion are that the problem is so complex that any theoretical approach is doomed to failure, and that the film is so thin, being inherently of molecular scale, that modeling the material as a continuum ceases to be valid. Due to the molecular orientation, the lubricant has an underlying microstructure. They turned to molecular dynamic simulation for help, from which macroscopic flow equations are drawn. This is also validated through molecular dynamic simulation by Hu et al. [6,7] and Mark et al. [8]. To date, experimental research had "got a little too far forward on its skis however, theoretical approaches have not had such rosy prospects as the experimental ones have. Theoretical modeling of the lubrication features associated with TFL is then urgently necessary. 

W. F. van Gunsteren and A. E. Mark, Validation of molecular dynamics simulation,... 

Daggett, V., Validation of protein-unfolding transition states identified in molecular dynamics simulations. Biochem Soc Symp, 2001(68) 83-93. 

The general method of molecular dynamics simulations is based on evaluation of the time history of positions and linear momenta for the ensemble of particles (atoms or molecules) subject to investigation. For classical systems it is assumed that the Bom-Oppenheimer approximation for separation of the electronic and nuclear degrees of freedom is valid and the evolution of the system takes place without changes in the electronic... 

Molecular dynamics simulations are attractive because they can provide not only quantitative information about rates and pathways of reactions, but also valuable insight into the details of ho y the chemistry occurs. Furthermore, a dynamical treatment is required if the statistical assumption is not valid. Yet another reason for interest in explicit atomic-level simulations of the gas-phase reactions is that they contribute to the formulation of condensed-phase models and, of course, are needed if one is to include the initial stages of the vapor-phase chemistry in the simulations of the decomposition of energetic materials. These and other motivations have lead to a lot of efforts to develop realistic atomic-level models that can be used in MD simulations of the decomposition of gas-phase energetic molecules. 

Sewell and co workers [145-148] have performed molecular dynamics simulations using the HMX model developed by Smith and Bharadwaj [142] to predict thermophysical and mechanical properties of HMX for use in mesoscale simulations of HMX-containing plastic-bonded explosives. Since much of the information needed for the mesoscale models cannot readily be obtained through experimental measurement, Menikoff and Sewell [145] demonstrate how information on HMX generated through molecular dynamics simulation supplement the available experimental information to provide the necessary data for the mesoscale models. The information generated from molecular dynamics simulations of HMX using the Smith and Bharadwaj model [142] includes shear viscosity, self-diffusion [146] and thermal conductivity [147] of liquid HMX. Sewell et al. have also assessed the validity of the HMX flexible model proposed by Smith and Bharadwaj in molecular dynamics studies of HMX crystalline polymorphs. 

We think that judicious application of molecular simulation tools for the calculation of thermophysical and mechanical properties is a viable strategy for obtaining some of the information required as input to mesoscale equations of state. Given a validated potential-energy surface, simulations can serve as a complement to experimental data by extending intervals in pressure and temperature for which information is available. Furthermore, in many cases, simulations provide the only realistic means to obtain key properties e.g., for explosives that decompose upon melting, measurement of liquid-state properties is extremely difficult, if not impossible, due to extremely fast reaction rates, which nevertheless correspond to time scales that must be resolved in mesoscale simulations of explosive shock initiation. By contrast, molecular dynamics simulations can provide converged values for those properties on time scales below the chemical reaction induction times. Finally,... 

The atomic radii may be further refined to improve the agreement between experimental and theoretical solvation free energies. Work on this direction has been done by Luque and Orozco (see [66] and references cited therein) while Barone et al. [67] defined a set of rules to estimate atomic radii. Further discussion on this point can be found in the review by Tomasi and co-workers [15], It must be noted that the parameterization of atomic radii on the basis of a good experiment-theory agreement of solvation energies is problematic because of the difficulty to separate electrostatic and non-electrostatic terms. The comparison of continuum calculations with statistical simulations provides another way to check the validity of cavity definition. A comparison between continuum and classical Monte Carlo simulations was reported by Costa-Cabral et al. [68] in the early 1980s and more recently, molecular dynamics simulations using combined quantum mechanics and molecular mechanics (QM/MM) force-fields have been carried out to analyze the case of water molecule in liquid water [69],... 

The above formula for Z, the NPT partition function, was first reported by Guggenheim [74], who wrote the expression down by analogy rather than based on a detailed derivation. While this form of the partition function is thought to be broadly valid and is widely applied (for example in molecular dynamics simulation [6]), it introduces the conceptual difficulty that the meaning of the discrete volumes Vi is not clear. Discrete energy states arise naturally from quantum statistics. Yet it is not necessarily obvious what discrete volumes to sum over in Equation (12.50). In fact for most applications it makes sense to replace the discrete sum with a continuous volume integral. Yet doing so results in a partition function that has units of volume, which is inappropriate for a partition function that formally should be unitless. 

The SHG results are at their most useful when they can be combined with other measurements and used to validate molecular dynamics simulations of the interface. 

Recendy, validity of the two assumptions regarding the free energy proflie, parabolic and solute independence of the force constants, has been examined by several authors. These assumptions have been predicted from the continuum dielecuic models and commonly adopted in many of the early works. Kakitani et alJ discussed the nonlinearity of solvation related to ET in polar solvents, and Carter and Hynes performed molecular dynamics simulations of the charge separation (CS) and the charge recombination (CR) reactions to observe such non-linear effects. More recently, Ando et alf discussed these problems and they observed no such non-linear effects. Due to the non-linear nature of the hypemetted chain (HNC) closure to solve the RISM equation, our method can shed light on the non-linearity of the free energy profiles. In section III, we apply our method, which is outlined briefly in section II, to the CS reaction which was previously studied by Carter and Hynes, and discuss the problems mentioned above based on the obtained free energy profiles. 

The kinematic model that is used to interpret the results of the molecular dynamics simulations has been validated by comparison to exact dynamical calculations for collisions of the isolated reactants, at high energies. The model assumes that the transition from reactants to products occurs in a sudden like manner up to a given configuration the motion is that of the unperturbed reactants beyond that configuration it is that of the final, free, products. 

Since the dielectric continuum representation of the solvent has significant limitations, the molecular dynamics simulation of PCET with explicit solvent molecules is also an important direction. One approach is to utilize a multistate VB model with explicit solvent interactions [34-36] and to incorporate transitions among the adiabatic mixed electronic/proton vibrational states with the Molecular Dynamics with Quantum Transitions (MDQT) surface hopping method [39, 40]. The MDQT method has already been applied to a one-dimensional model PCET system [39]. The advantage of this approach for PCET reactions is that it is valid in the adiabatic and non-adiatic limits as well as in the intermediate regime. Furthermore, this approach is applicable to PCET in proteins as well as in solution. 

Gomes, C.J., M. Madrid, and C.H. Amon. Parallel Molecular Dynamics Code Validation Through Bulk Silicon Thermal Conductivity Calculations, in Proceedings of the 2003 ASME International Mechanical Engineering Congress and Exposition, IMECE 2003-42352. 2003. Washington, DC. Lee, Y.H., R. Biswas, C.M. Soukoulis, C.Z. Wang, C.T. Chan, and K.M. Ho, Molecular-Dynamics Simulation of Thermal Conductivity in Amorphous Silicon. Physical Review B, 1991.43(8) p. 6573-6580. 

---