Interpretation of atomic motion in flexible molecules: accelerating molecular dynamics simulations

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DOIResolve DOI: http://doi.org/10.1103/PhysRevE.85.026706
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TypeArticle
Journal titlePhysical Review E - Statistical, Nonlinear, and Soft Matter Physics
ISSN1539-3755
Volume85
Issue2
Article number26706
SubjectConformational properties; Coriolis; Femtoseconds; Molecular dynamics simulations; Multiple time step; Picoseconds; Time step; Translational degrees of freedoms; Vibrational components; Vibrational motions; Water models; Degrees of freedom (mechanics); Kinetic energy; Molecular dynamics; Molecules; Atoms
AbstractWe propose a new approach to split up the velocities of atoms of flexible molecules into translational, rotational, and vibrational components. As a result, the kinetic energy of the system can easily be expressed in terms of only three parts related to the above components. This is distinct from the standard Eckart method, where the cumbersome Coriolis contribution to the kinetic energy appears additionally. The absence of such a contribution within the proposed approach allows us to readily extend the microcanonical multiple-time-step dynamics of flexible molecules to the canonical-isokinetic Nosé-Hoover chain ensemble by explicitly integrating the translational, orientational, and vibrational motion. The previous extensions dealt exclusively with translational degrees of freedom of separate atoms, leading to a limitation on the size of the outer time step of 100 femtoseconds. We show on molecular dynamics simulations of the flexible TIP3P water model that the new canonical-isokinetic formulation gives a possibility to significantly overcome this limitation. In particular, huge outer time steps of order from a few hundred femtoseconds up to several picoseconds can now be employed to study conformational properties without loss of accuracy.
Publication date
LanguageEnglish
AffiliationNational Research Council Canada (NRC-CNRC); National Institute for Nanotechnology
Peer reviewedYes
NPARC number21270276
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Record identifier25a19bf1-b940-46a8-b61e-3eb8939911a2
Record created2014-01-20
Record modified2016-05-09
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