title: Optimization of Monte Carlo trial moves for protein simulations.
abstract: Closed rigid-body rotations of residue segments under bond-angle restraints are simple and effective Monte Carlo moves for searching the conformational space of proteins. The efficiency of these moves is examined here as a function of the number of moving residues and the magnitude of their displacement. It is found that the efficiency of folding and equilibrium simulations can be significantly improved by tailoring the distribution of the number of moving residues to the simulation temperature. In general, simulations exploring compact conformations are more efficient when the average number of moving residues is smaller. It is also demonstrated that the moves do not require additional restrictions on the magnitude of the rotation displacements and perform much better than other rotation moves that do not restrict the bond angles a priori. As an example, these results are applied to the replica exchange method. By assigning distributions that generate a smaller number of moving residues to lower temperature replicas, the simulation times are decreased as long as the higher temperature replicas are effective.
authors.affiliation: Department of Physics, Indiana University Purdue University Indianapolis, 402 N. Blackford St., LD156-J Indianapolis, Indiana 46202, USA. mbetancourt@mailaps.org
authors.forename: Marcos R
authors.initials: MR
authors.lastname: Betancourt
mesh_terms: D008956:Models, Chemical; D009010:Monte Carlo Method; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D011506:Proteins