Work

Potential energy function and parameters for simulations of the molecular dynamics of proteins and nucleic acids in solution

Year: 1995

Type: article

Abstract: We present the complete set of energy parameters used in the ENCAD (Energy Calculation and Dynamics) simulation program [J. Mol. Biol. 168 (1983) 595]. Full details are given of the form of the potential, which has been designed for efficient simulation of trajectories of macromolecules in solution. Emphasis is placed on energy conservation and the nonbonded truncation schemes needed to achieve it. Simulations of macromolecules in solution with ENCAD are both very stable in that the native structure is preserved at room temperature and efficient in that nanosecond simulations take a few weeks on an ordinary workstation.

Source: Computer Physics Communications

DOI: 10.1016/0010-4655(95)00049-l

Authors: Michael Levitt, Miriam Hirshberg, Ruth Sharon, Valerie Daggett

Institutions: Stanford Medicine, Stanford University

Language: English

Topic: Protein Structure and Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $4,160

Funders: National Science Foundation, Jane Coffin Childs Memorial Fund for Medical Research