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Quasi‐Hamiltonian equations of motion for internal coordinate molecular dynamics of polymers
Author(s) -
Mazur Alexey K.
Publication year - 1997
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/(sici)1096-987x(199708)18:11<1354::aid-jcc3>3.0.co;2-k
Subject(s) - molecular dynamics , bond length , hamiltonian (control theory) , cartesian coordinate system , equations of motion , degrees of freedom (physics and chemistry) , molecular geometry , coordinate system , classical mechanics , statistical physics , chemistry , physics , computational chemistry , mathematics , geometry , molecule , quantum mechanics , mathematical optimization
Conventional molecular dynamics simulations of macromoleculesrequire long computational times because the most interesting motions arevery slow compared to the fast oscillations of bond lengths and bond anglesthat limit the integration time step. Simulation of dynamics in the spaceof internal coordinates, that is, with bond lengths, bond angles, andtorsions as independent variables, gives a theoretical possibility ofeliminating all uninteresting fast degrees of freedom from the system. Thisarticle presents a new method for internal coordinate molecular dynamicssimulations of macromolecules. Equations of motion are derived that areapplicable to branched chain molecules with any number of internal degreesof freedom. Equations use the canonical variables and they are much simplerthan existing analogs. In the numerical tests the internal coordinatedynamics are compared with the traditional Cartesian coordinate moleculardynamics in simulations of a 56 residue globular protein. For the firsttime it was possible to compare the two alternative methods on identicalmolecular models in conventional quality tests. It is shown that thetraditional and internal coordinate dynamics require the same time stepsize for the same accuracy and that in the standard geometry approximationof amino acids, that is, with fixed bond lengths, bond angles, and rigidaromatic groups, the characteristic step size is 4 fs, which is 2 timeshigher than with fixed bond lengths only. The step size can be increased upto 11 fs when rotation of hydrogen atoms is suppressed. © 1997 byJohn Wiley & Sons, Inc. J Comput Chem 18 :1354–1364, 1997