NVU dynamics. III. Simulating molecules at constant potential energy
نویسندگان
چکیده
منابع مشابه
NVU dynamics. III. Simulating molecules at constant potential energy.
This is the final paper in a series that introduces geodesic molecular dynamics at constant potential energy. This dynamics is entitled NVU dynamics in analogy to standard energy-conserving Newtonian NVE dynamics. In the first two papers [T. S. Ingebrigtsen, S. Toxvaerd, O. J. Heilmann, T. B. Schrøder, and J. C. Dyre, J. Chem. Phys. 135, 104101 (2011); T. S. Ingebrigtsen, S. Toxvaerd, T. B. Sch...
متن کاملNVU dynamics. I. Geodesic motion on the constant-potential-energy hypersurface.
An algorithm is derived for computer simulation of geodesics on the constant-potential-energy hypersurface of a system of N classical particles. First, a basic time-reversible geodesic algorithm is derived by discretizing the geodesic stationarity condition and implementing the constant-potential-energy constraint via standard Lagrangian multipliers. The basic NVU algorithm is tested by single-...
متن کاملHigh-performance molecular dynamics at constant pH and constant redox potential using AMBER
Protein function is intrinsically related to structure and dynamic. Solution pH often has a dramatic impact on protein systems, since pH can affect the charge distribution within these biomolecules.[1] Understanding how pH-dependent conformation changes take place is key to the development of drugs targeting pH sensors, to the success of computational drug discovery strategies, and so forth.[2]...
متن کاملMolecular dynamics at constant temperature and pressure.
approved: enri J.F. Jansen Molecular dynamics is a technique in which the trajectories of a group of particles are calculated as a function of time by integrating the equations of motion. In this thesis we study the use of molecular dynamics for atoms in a crystal. A model is introduced which describes interactions of a physical system with an external heat reservoir in molecular dynamics simul...
متن کاملAnalytic potential energy functions for simulating aluminum nanoparticles.
Potential energy functions (PEFs) parametrized to bulk data are shown to perform poorly for small aluminum nanoparticles and clusters. In contrast, PEFs parametrized to a limited set of cluster and bulk data, but no nanoparticle data, perform well for nanoparticles. This validates a practical scheme for developing PEFs for nanoscale systems. Building on these findings, we optimized five PEFs by...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2012
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.4768957