For example, instead of treating all four atoms of a CH 3 methyl group explicitly or all three atoms of CH 2 methylene group , one represents the whole group with one pseudo-atom. It must, of course, be properly parameterized so that its van der Waals interactions with other groups have the proper distance-dependence.
Similar considerations apply to the bonds, angles, and torsions in which the pseudo-atom participates. In this kind of united atom representation, one typically eliminates all explicit hydrogen atoms except those that have the capability to participate in hydrogen bonds polar hydrogens.
The polar hydrogens are usually retained in the model, because proper treatment of hydrogen bonds requires a reasonably accurate description of the directionality and the electrostatic interactions between the donor and acceptor groups. A hydroxyl group, for example, can be both a hydrogen bond donor, and a hydrogen bond acceptor, and it would be impossible to treat this with one OH pseudo-atom.
About half the atoms in a protein or nucleic acid are non-polar hydrogens, so the use of united atoms can provide a substantial savings in computer time. In many simulations of a solute-solvent system the main focus is on the behavior of the solute with little interest of the solvent behavior particularly in those solvent molecules residing in regions far from the solute molecule.
The use of non-rectangular periodic boundary conditions, stochastic boundaries and solvent shells can all help reduce the number of solvent molecules required and enable a larger proportion of the computing time to be spent instead on simulating the solute. It is also possible to incorporate the effects of a solvent without needing any explicit solvent molecules present. One example of this approach is to use a potential mean force PMF which describes how the free energy changes as a particular coordinate is varied.
The free energy change described by PMF contains the averaged effects of the solvent. Examples include charge-charge interactions between ions and dipole-dipole interactions between molecules. Modelling these forces presents quite a challenge as they are significant over a distance which may be larger than half the box length with simulations of many thousands of particles. Though one solution would be to significantly increase the size of the box length, this brute force approach is less than ideal as the simulation would become computationally very expensive.
Spherically truncating the potential is also out of the question as unrealistic behaviour may be observed when the distance is close to the cut off distance. Steered molecular dynamics SMD simulations, or force probe simulations, apply forces to a protein in order to manipulate its structure by pulling it along desired degrees of freedom.athmensupa.ml
ESDW in Quantum dynamics
These experiments can be used to reveal structural changes in a protein at the atomic level. SMD is often used to simulate events such as mechanical unfolding or stretching. There are two typical protocols of SMD: one in which pulling velocity is held constant, and one in which applied force is constant. Typically, part of the studied system e. Forces are then applied to specific atoms at either a constant velocity or a constant force.
Umbrella sampling is used to move the system along the desired reaction coordinate by varying, for example, the forces, distances, and angles manipulated in the simulation. Through umbrella sampling, all of the system's configurations—both high-energy and low-energy—are adequately sampled. Then, each configuration's change in free energy can be calculated as the potential of mean force. A lot of important applications of SMD are in the field of drug discovery and biomolecular sciences.
For e. SMD was used to investigate the stability of Alzheimer's protofibrils,  to study the protein ligand interaction in cyclin-dependent kinase 5  and even to show the effect of electric field on thrombin protein and aptamer nucleotide complex  among many other interesting studies. The following biophysical examples illustrate notable efforts to produce simulations of a systems of very large size a complete virus or very long simulation times up to 1.
From Wikipedia, the free encyclopedia. Computer simulations to discover and understand chemical properties. Main articles: Interatomic potential , Force field , and Comparison of force field implementations. Main article: Force field. Main articles: Quantum chemistry and List of quantum chemistry and solid state physics software. Molecular modeling Computational chemistry Force field chemistry Comparison of force field implementations Monte Carlo method Molecular design software Molecular mechanics Multiscale Green's function Car—Parrinello method Comparison of software for molecular mechanics modeling Quantum chemistry Discrete element method Comparison of nucleic acid simulation software Molecule editor.
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