Molecular dynamics

Monday, December 8, 2008 - 11:50am - 12:30pm
Alfonso De Simone (University of Cambridge)
Water at the surface of proteins plays a crucial biological
role. The study of hydration is therefore fundamental for
achieving a complete description of key factors determining the
protein biology. In this framework, Molecular Dynamics
simulations have provided precious tools for elucidating the
structure and dynamics of waters in the protein hydration
shell. We employed Molecular Dynamics to address on the
hydration properties of the Prion Protein, whose misfolding and
aggregation is associated to Transmissible Spongiform
Tuesday, December 9, 2008 - 9:00am - 9:40am
Jiali Gao (University of Minnesota, Twin Cities)
Traditionally, molecular dynamics and Monte Carlo simulations of
condensed phase systems including biopolymers are carried out using molecular mechanics or force fields that describe intermolecular interactions. In fact, the formalism of these force fields for biomolecular simulatiosn was established in the 1960s. Although the computational accuracy has increased
enormously through parameterization, little has changed in
the functional terms used in the force fields. In this talk, I will describe an explicit polarization
Thursday, November 6, 2008 - 11:00am - 11:45am
Raymond Kapral (University of Toronto)
Modeling the dynamics of complex molecular systems is difficult
since physically relevant distance and time scales are
often very long. Consequently, a variety of different coarse-grained
molecular dynamics methods, which attempt to bridge gap between short
and long scales, has been developed. The talk will focus one
such method, multiparticle colision dynamics, for the computation of
the mesoscopic dynamics of molecular systems.
In particular, polymer and biopolymer dynamics in crowded molecular
Tuesday, November 4, 2008 - 10:30am - 11:15am
Christof Schütte (Freie Universität Berlin)
No Abstract
Wednesday, February 24, 2016 - 11:00am - 11:25am
Paul Patrone (National Institute of Standards and Technology)
One of the key observations underpinning the theory of molecular dynamics (MD) is the formal mathematical result that discrete time-stepping, symplectic integrators conserve energy. From the standpoint of model verification, this property is crucial if MD algorithms are to describe the statistics of thermodynamic systems. Nonetheless, practical implementations of MD always exhibit some level of energy drift, and it is not clear to what extent this affects simulated predictions.
Thursday, January 10, 2008 - 3:00pm - 4:00pm
Michael Levitt (Stanford University)
Lecture 2 will describe the complementary methods of simulation: molecular dynamics and normal mode dynamic. We will show how they help understand the stability and the nature of protein motion.
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