Molecular dynamics simulations using

D. Fincham and B. J. Ralston, Molecular dynamics simulation using the Cray-1 vector processing computer , Comp. Phys. Comm., Vol 23, no 2, 127-34, 1981. 

IlypcrChem cannot perform a geometry optinii/.aiioii or molecular dynamics simulation using Cxien ded Iliickel. Stable molecules can collapse, with nuclei piled on top of one another, or they can dissociate in to atoms. With the commonly used parameters, the water molecule is predicted to be linear. 

A molecular dynamics simulation used for a conformational search can provide a quick assessment of low energy conformers suitable for further analysis. Plot the average potential energy of the molecule at each geometry. This plot may also suggest conformational changes in a molecule. 

Dimitrov, D. 1., Milchev, A. and Binder, K (2007) Polymer brushes in solvents of variable quality Molecular dynamics simulations using explicit solvent./. Chem. Phys., 127, 084905. 

Figure 5-2. Plot of CsOsCiOi angle of non-reducing saccharide residue 4-0-a -D-xylopyranosyl-a -D-xylopyranose from QM/MM molecular dynamics simulations using (a) a PM3/TIP3P potential and (b) a PM3CARB-1/TIP3P potential. Reproduced with permission from reference [66]. Copyright Elsevier 2004...

Keffer DJ, Mintmire JW (2000) Efficient parallel algorithms for molecular dynamics simulations using variable charge transfer electrostatic potentials. Int J Quant Chem 80(4-5) 733-742... 

Patel S, Mackerell AD, Brooks CL (2004) CHARMM fluctuating charge force field for proteins II -Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J Comput Chem 25(12) 1504-1514... 

Patel S, Brooks CL (2005) Structure, thermodynamics, and liquid-vapor equilibrium of ethanolfrom molecular-dynamics simulations using nonadditive interactions. J Chem Phys 123(16) 164502... 

Patel S, Brooks CL (2006) Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials. J Chem Phys 124(20) 204706... 

Park, S. Khalili-Araghi, F. Tajkhorshid, E. Schulten, K., Free energy calculation from steered molecular dynamics simulations using Jarzynski s equality, J. Chem. Phys. 

Poly butadiene Mode-Coupling Theory Analysis of Molecular Dynamics Simulations Using a Chemically Realistic Model. 

Calhoun and Voth also utilized molecular dynamic simulations using the Anderson-Newns Hamiltonian to determine the free energy profile for an adiabatic electron transfer involving an Fe /Fe redox couple at an electrolyte/Pt(lll) metal interface. This treatment expands upon their earlier simulation by including, in particular, the influence of the motion of the redox ions and the counterions at the interface. 

The dielectric and mechanical relaxations on poly(l,3-dioxan-5yl-methacrylate) (PDMA) [104], show that this polymer present a variety of absorptions due to the versatility of its structural moiety [105]. Recently this behavior have been studied by molecular dynamic simulation using different methods and force fields [106-109], These polymers are analyzed from molecular simulation using different ways but... 

O.A. Karim et al., The ice/water interface A molecular dynamics simulation using the simple point charge model. J. Chem. Phys. 92, 4634 1635 (1990)... 

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. 

Electron-hole pairs have already been treated on the Hartree-Fock level in otherwise classical high-dimensional molecular dynamics simulation using the molecular dynamics with electronic friction method [120]. In this approach, the energy transfer between nuclear degrees of freedom and the electron bath of the surface is also modelled with a position-dependent friction term, but additionally temperature-dependent fluctuating forces are included. 

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],... 

Parallel Algorithms for Molecular Dynamics Simulations Using Variable Charge Transfer Electrostatic Potentials. 

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