Classical Molecular Dynamics

2006

2010

The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large systems are presented. Both tasks lead to time consuming simulations that require massively parallel high performance computing. In the present work, new

Molecular-dynamics simulations provide reliable infor-mation about the microscopic behavior of the investigated systems by numerical solution of the equations of motion. The constantly growing computer performance (in particular, the number of computing cores) makes wider the range of research topics – and systems – accessible by these means. However, simulation continu-ance increases drastically with the size of the systems and the scalability of the most popular simulation packages worsens. We aim at the development of a multiple step-size symplectic integrator adapted to the large biomolecular systems particular features, such as multiple frequency modes, interaction hierarchy and strong inhomogeneity. To this end. we analyze the scalability and the work-load increase and distribution among the computing cores in the packages GROMACS and NAMD on the example of three test systems with increasing size (5xl0 5 ~10 6 and ~2.2x10 6 atoms respectively), by means of the GROMAC S in-buil...

Journal of Computational Chemistry, 1997

2003

We review recent progress in understanding fundamental processes in biology, chemistry and physics on the basis of ab initio and molecular dynamics simulations. The first step of the visual process involving the excitation of bovine rhodopsin after absorption of light is taken as an example from biochemistry to demonstrate what is nowadays possible to simulate numerically. The act of freezing of water has recently been simulated, for the first time successfully, by scientists from chemistry. Martensitic transformation in bulk and nanophase materials, a typical and hitherto not completely solved problem from solid state physics, is used to illustrate the achievements of multimillion atoms simulations. 9.1 Molecular Dynamics as a Multidisciplinary Numerical Tool Molecular dynamics (MD) has proved to be an optimum numerical recipe applicable to problems with many degrees of freedom from quite different fields of science. The knowledge of the energy or potential landscape of interacting...

SIAM Journal on Scientific Computing, 2012