Potential Function Parameter Development Workshop - Feb. 16, 2005

The Center for Structural Biology will hold a workshop on the development of potential function parameters for use in molecular mechanics calculations. This workshop, instructed by Professor Terry Lybrand, is aimed at researchers who wish to use molecular mechanics techniques to investigate the structure and behavior of biomolecular systems.

Molecular mechanics has become a popular computational strategy, particularly for the study of molecules like proteins or synthetic polymers, in large measure due to tractability of molecular mechanics calculations for these systems. However, the relative computational efficiency of molecular mechanics calculations comes with a price: suitable potential function parameters must be available for all molecules and residues in a molecular system before molecular mechanics calculations can be performed. In the absence of potential function parameters, calculations literally cannot be performed, while poorly derived or arbitrarily chosen parameters will yield highly suspect, and possibly even physically unreasonable results.

Enrollment info

The fee for this workshop is $100. The workshop is open to registration for Vanderbilt students, faculty, and staff.

Advance registration is required due to limited capacity in the molecular modeling teaching lab. Enrollment is limited to 15 people on a first-come, first-served basis. Therefore, register early to ensure the availability of your seat.

Workshop Syllabus

The three-hour workshop will be held Wednesday Feb 16 from 1:30-4:30PM, hosted in the College of Arts and Science Molecular Modeling Teaching Laboratory (5119 Stevenson Center).

In this workshop, we will discuss briefly the underlying philosophy and basic details of molecular mechanics potential functions, with a particular emphasis on potential functions typically used for calculations of large biomolecules. Topics covered will include:

  • The mathematical expressions used in typical potential functions
  • The physical justification for these expressions
  • Strategies and procedures for development of suitable potential function parameters
  • Applications and limitations of typical potential functions used for biomacromolecular calculations.