An open problem in numerical analysis is to explain why molecular dynamics works. The difficulty is that numerical trajectories are only accurate for very short times, whereas the simulations are performed over long time intervals. It is believed that statistical information from these simulations is accurate, but no one has offered a rigourous proof of this. In order to give mathematicians a c...

The ab initio atom-centered density matrix propagation (ADMP) and the quantum wavepacket ab initio molecular dynamics (QWAIMD) computational methods are briefly described. Studies on vibrational and electronic properties obtained utilizing these methods are highlighted. ∗ [email protected]

Ab initio calculations are used to calculate the atomic charges in the selectivity filter part of KcsA potassium channel according to the Merz–Kollman–Singh scheme. On the basis of a long molecular dynamics simulation, we show that these charges deviate significantly from the values usually implemented in the most common force fields. These consequent changes may considerably influence our view...

We present a nonlinear dynamical model for DNA thermal denaturation, which is based on the finite stacking enthalpies used in thermodynamical nearest-neighbour calculations. Within this model, the finiteness of stacking enthalpies is shown to be responsible for the sharpness of calculated melting curves. Transfer-integral and molecular dynamics calculations are performed to demonstrate that the...

This paper introduces MD, a complete high-performance parallel molecular dynamics simulation system. MD eeciently manages the control and data ow required for the basic molecular dynamics calculations as well as for global statistics and scientiic visualization. We brieey examine the structure of MD, present an analysis of its performance for several physical systems, and examine ways in which ...

Ferdinand Jamitzky Leibniz Supercomputing Centre (LRZ) Boltzmannstrasse 1 85748 Garching, Germany [email protected] Helmut Satzger Leibniz Supercomputing Centre (LRZ) Boltzmannstrasse 1 85748 Garching, Germany [email protected] Gerald Mathias Ludwig-MaximiliansUniversität München, Lehrstuhl für BioMolekulare Optik Oettingenstrasse 67 80538 München, Germany [email protected]...

This paper focuses on the use of real-time visualization and computational steering techniques in molecular dynamics (MD) simulations of problems in materials science. Simulations of nanoindentation are mainly used to illustrate the interplay between the computational steering, realtime visualization and the scientific discovery process. We will describe a VTK based viewer that we have develope...

Shear deformations of Cu57Zr43 bulk metallic glass (BMG) model systems are performed using molecular dynamics simulation. The results suggest that both the hydrostatic stress and the stress normal to the shear plane should affect the shear response (modified Mohr–Coulomb yield criterion). We see shear localization and shear band nucleation in both a small system of 2000 atoms, and large systems...

Predicting the structural and electronic properties of complex systems is one of the outstanding problems in condensed matter physics. Central to most methods used in molecular dynamics is the repeated solution of large eigenvalue problems. This paper reviews the source of these eigenvalue problems, describes some techniques for solving them, and addresses the diiculties and challenges which ar...