Long time dynamics of a polymer with rigid body monomer units relating to a protein model: Comparison with the rouse model

✍ Scribed by E.W. Knapp

• Publisher: John Wiley and Sons
• Year: 1992
• Tongue: English
• Weight: 572 KB
• Volume: 13
• Category: Article
• ISSN: 0192-8651
• DOI: 10.1002/jcc.540130702

✦ Synopsis

Simulation data from an off-lattice polymer model are compared with data from the Rouse model. The polymer model is built of sequentially connected rigid monomer units that represent the amide planes of a protein backbone. The time propagation of the dynamics of the polymer model is performed by a Monte Carlo method. The elementary Monte Carlo steps correspond to local conformational changes in a window of three consecutive monomer units. The time autocorrelation functions of end-to-end distances from segments within the linear chain molecule are considered in detail. Both models exhibit a stretched exponential decay pattern. A comparison of the data from the Rouse model and the computer simulation provide an estimate of the time unit of 15 ps for a full scan of the algorithm for local conformational changes along the chain. With a conservative estimate of the parameters governing the Rouse model this time unit is four orders of magnitude longer than the elementary time step of a conventional computer simulation of polymer dynamics based upon the classical equations of motion for all atoms.