Time-dependent distance restraints in molecular dynamics simulations

✍ Scribed by Andrew E. Torda; Ruud M. Scheek; Wilfred F. van Gunsteren

• Publisher: Elsevier Science
• Year: 1989
• Tongue: English
• Weight: 511 KB
• Volume: 157
• Category: Article
• ISSN: 0009-2614
• DOI: 10.1016/0009-2614(89)87249-5

✦ Synopsis

A method for enforcing nuclear Overhauser effect (NOE) distance restraints in molecular dynamics simulations is presented. Rather than model the NOE distance as static, a term is included in the force field such that the distance restraint need only be satisfied as a (r-j} -'I3 weighted time average over the simulation trajectory. This provides a better approximation of the physical nature of the NOE and reduces the disturbance lo the force field due to the artificial term. Tests on a simple model system demonstrate the inadequacy of current methods and show the advantages of this novel approach, resulting in a more extensive search of conformational space.