Unconstrained molecular dynamics

H6nin, J. Chipot, C., Overcoming free energy barriers using unconstrained molecular dynamics simulations, J. Chem. Phys. 2004, 727, 2904-2914... 

These difficulties can be circumvented by using the adaptive biasing force (ABF) method of Darve, Pohorille, and coworkers [18, 28, 29], which is based on unconstrained molecular dynamics simulations. This is a very efficient approach which begins by establishing a simple formula to calculate d,4/d from regular molecular dynamics in which is not constrained. This derivative represents the mean force acting on . Therefore if we remove this force from the system we obtain... 

To complement H-NMR studies, an extended molecular dynamics simulation of 58 was carried out. The starting geometry for 58 was generated using coordinates taken from the partially helical, C-terminal decapeptide portion (residues 27-36) of the NPY model shown in Plate 13. The residues corresponding to Thr-32 and Gln-34 were replaced with Tyr and Leu, respectively, and subjected to an unconstrained molecular dynamics simulation. The structures obtained from this simulation (a representative structure is shown in Plate 15b) share several important features with those observed by H-NMR, specifically the formation of an Asx turn and close association of the aromatic tyrosine rings. 

Standard unconstrained molecular dynamics simulations have been used extensively to model the folding and unfolding of protein systems [97-99]. In... 

The energetic stabilization of a proton in a membrane provided by a proton wire raises a question about the likelihood of the spontaneous formation of such wires. This issue was addressed in separate calculations in which the free energy of a chain of water molecules spanning the bilayer was estimated at approximately 25 kcal/mol [14]. In unconstrained molecular dynamics simulations it was further found that transmembrane water chains are very transient, with lifetimes of only a few picoseconds. These lifetimes are much shorter that the time required for the water reorientation in the chain needed to transfer another pro-... 

In the present work, we report on a new semi-empirical theoretical approach which allows us to perform spin and symmetry unconstrained total energy calculations for clusters of transition metal atoms in a co .putationally efficient way. Our approach is based on the Tight Binding Molecular Dynamics (TBMD) method. 

The scheme we employ uses a Cartesian laboratory system of coordinates which avoids the spurious small kinetic and Coriolis energy terms that arise when center of mass coordinates are used. However, the overall translational and rotational degrees of freedom are still present. The unconstrained coupled dynamics of all participating electrons and atomic nuclei is considered explicitly. The particles move under the influence of the instantaneous forces derived from the Coulombic potentials of the system Hamiltonian and the time-dependent system wave function. The time-dependent variational principle is used to derive the dynamical equations for a given form of time-dependent system wave function. The choice of wave function ansatz and of sets of atomic basis functions are the limiting approximations of the method. Wave function parameters, such as molecular orbital coefficients, z,(f), average nuclear positions and momenta, and Pfe(0, etc., carry the time dependence and serve as the dynamical variables of the method. Therefore, the parameterization of the system wave function is important, and we have found that wave functions expressed as generalized coherent states are particularly useful. A minimal implementation of the method [16,17] employs a wave function of the form ... 

In summary, ab initio and hybrid QM/MM molecular dynamics studies provide a valuable tool for the investigation of photoinduced CTI. Excited-state MD simulations of two small organic molecules, PSB5 and formaldimine, were carried out in order to assess the performance of different excited-state methods for the description of cis-trans isomerization reactions. In contrast to the majority of previous studies of the same model systems, our approach has the advantage to allow a completely unconstrained and unbiased relaxation of the excited molecule on its (3N-6)-dimensional PES. 

A molecular dynamics study based on an atomistic model with translations and rotations unconstrained in three dimensions was conducted together with heat capacity measurements [232] a more complete account of the simulation part was given in Ref. 340, and essentially the same model was... 

The physical effects of introducing constraints into a molecular model have been discussed by several authors. > This chapter is concerned mainly with the methods of constraint dynamics. In addition to descriptions of bond-stretch and angle-bend constraints, dihedral (or torsional) constraints are explicitly considered. Torsional modes generally have frequencies comparable to those of other modes, and the weak coupling condition is not satisfied in this case. Hence the constraint approximation is not justified for torsion. This fact is particularly important because torsional motions play a major role in conformation interconversion in small molecules as well as polymers, and constraining them can seriously alter the dynamics of the original, unconstrained system. 

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