Contents 1 Molecular mechanics 2 Variables 2.1 Coordinate representations 3 Applications 4 See also 5 Notes 6 External links Molecular mechanics[edit]
E = E bonds + E angle + E dihedral + E non-bonded displaystyle E=E_ text bonds +E_ text angle +E_ text dihedral +E_ text non-bonded , E non-bonded = E electrostatic + E van der Waals displaystyle E_ text non-bonded =E_ text electrostatic +E_ text van der Waals , This function, referred to as a potential function, computes the molecular potential energy as a sum of energy terms that describe the deviation of bond lengths, bond angles and torsion angles away from equilibrium values, plus terms for non-bonded pairs of atoms describing van der Waals and electrostatic interactions. The set of parameters consisting of equilibrium bond lengths, bond angles, partial charge values, force constants and van der Waals parameters are collectively termed a force field. Different implementations of molecular mechanics use different mathematical expressions and different parameters for the potential function. The common force fields in use today have been developed by using high level quantum calculations and/or fitting to experimental data. The method, termed energy minimization, is used to find positions of zero gradient for all atoms, in other words, a local energy minimum. Lower energy states are more stable and are commonly investigated because of their role in chemical and biological processes. A molecular dynamics simulation, on the other hand, computes the behaviour of a system as a function of time. It involves solving Newton's laws of motion, principally the second law, F = m a displaystyle mathbf F =mmathbf a . Integration of Newton's laws of motion, using different integration
algorithms, leads to atomic trajectories in space and time. The force
on an atom is defined as the negative gradient of the potential energy
function. The energy minimization method is useful to obtain a static
picture for comparing between states of similar systems, while
molecular dynamics provides information about the dynamic processes
with the intrinsic inclusion of temperature effects.
Variables[edit]
Molecules can be modelled either in vacuum, or in the presence of a
solvent such as water. Simulations of systems in vacuum are referred
to as gas-phase simulations, while those that include the presence of
solvent molecules are referred to as explicit solvent simulations. In
another type of simulation, the effect of solvent is estimated using
an empirical mathematical expression; these are termed implicit
solvation simulations.
Coordinate representations[edit]
Most force fields are distance-dependent, making the most convenient
expression for these Cartesian coordinates. Yet the comparatively
rigid nature of bonds which occur between specific atoms, and in
essence, defines what is meant by the designation molecule, make an
internal coordinate system the most logical representation. In some
fields the IC representation (bond length, angle between bonds, and
twist angle of the bond as shown in the figure) is termed the Z-matrix
or torsion angle representation. Unfortunately, continuous motions in
Cartesian space often require discontinuous angular branches in
internal coordinates, making it relatively hard to work with force
fields in the internal coordinate representation, and conversely a
simple displacement of an atom in Cartesian space may not be a
straight line trajectory due to the prohibitions of the interconnected
bonds. Thus, it is very common for computational optimizing programs
to flip back and forth between representations during their
iterations. This can dominate the calculation time of the potential
itself and in long chain molecules introduce cumulative numerical
inaccuracy. While all conversion algorithms produce mathematically
identical results, they differ in speed and numerical accuracy.[1]
Currently, the fastest and most accurate torsion to Cartesian
conversion is the Natural Extension Reference Frame (NERF) method.[1]
Applications[edit]
Cheminformatics
Comparison of force field implementations
Comparison of nucleic acid simulation software
Comparison of software for molecular mechanics modeling
Density functional theory software
List of molecular graphics systems
List of protein structure prediction software
List of software for Monte Carlo molecular modeling
List of software for nanostructures modeling
Molecular design software
Molecular engineering
Molecular graphics
Molecular model
Molecular modeling on GPU
Notes[edit] ^ a b Parsons, J., Holmes, J. B., Rojas, J. M., Tsai, J., Strauss, C. E., Practical conversion from torsion space to cartesian space for in silico protein synthesis. [1] J Comput Chem 26 (2005), 1063-1068.[2] M. P. Allen, D. J. Tildesley, Computer simulation of liquids, 1989, Oxford University Press, ISBN 0-19-855645-4. A. R. Leach, Molecular Modelling: Principles and Applications, 2001, ISBN 0-582-38210-6 D. Frenkel, B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, 1996, ISBN 0-12-267370-0 D. C. Rapaport, The Art of Molecular Dynamics Simulation, 2004, ISBN 0-521-82568-7 R. J. Sadus, Molecular Simulation of Fluids: Theory, Algorithms and Object-Orientation, 2002, ISBN 0-444-51082-6 K.I.Ramachandran, G Deepa and Krishnan Namboori. P.K. Computational Chemistry and Molecular Modeling Principles and Applications 2008 [3] ISBN 978-3-540-77302-3 Springer-Verlag GmbH External links[edit] Center for Molecular Modeling at the National Institutes of Health (NIH) (U.S. Government Agency) Molecular Simulation, details for the Molecular Simulation journal, ISSN 0892-7022 (print), ISSN 1029-0435 (online) The eCheminfo Network and Community of Practice in Informatics and Modeling Molecular Modelling |