title: An improved replica-exchange sampling method: temperature intervals with global energy reassignment.
abstract: In a molecular dynamics (MD) simulation, representative sampling over the entire phase space is desired to obtain an accurate canonical distribution at a given temperature. For large molecules, such as proteins, this is problematic because systems tend to become trapped in local energy minima. The extensively used replica-exchange molecular dynamics (REMD) simulation technique overcomes this kinetic-trapping problem by allowing Boltzmann-weighted configuration exchange processes to occur between numerous thermally adjacent and compositionally identical simulations that are thermostated at sequentially higher temperatures. While the REMD method provides much better sampling than conventional MD, there are two substantial difficulties that are inherent in its application: (1) the large number of replicas that must be used to span a designated temperature range and (2) the subsequent long time required for configurations sampled at high temperatures to exchange down for potential inclusion within the low-temperature ensemble of interest. In this work, a new method based on temperature intervals with global energy reassignment (TIGER) is presented that overcomes both of these problems. A TIGER simulation is conducted as a series of short heating-sampling-quenching cycles. At the end of each cycle, the potential energies of all replicas are simultaneously compared at the same temperature using a Metropolis sampling method and then globally reassigned to the designated temperature levels. TIGER is compared with regular MD and REMD methods for the alanine dipeptide in water. The results indicate that TIGER increases sampling efficiency while substantially reducing the number of central processing units required for a comparable conventional REMD simulation.
authors.affiliation: Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, USA.
authors.forename: Xianfeng
authors.initials: X
authors.lastname: Li
authors.forename: Christopher P
authors.initials: CP
authors.lastname: O'Brien
authors.forename: Galen
authors.initials: G
authors.lastname: Collier
authors.forename: Nadeem A
authors.initials: NA
authors.lastname: Vellore
authors.forename: Feng
authors.initials: F
authors.lastname: Wang
authors.forename: Robert A
authors.initials: RA
authors.lastname: Latour
authors.forename: David A
authors.initials: DA
authors.lastname: Bruce
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Stuart
mesh_terms: D003198:Computer Simulation; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D013696:Temperature; D013816:Thermodynamics; D014867:Water / Q000737:chemistry*
chemical_list: D010455:Peptides; D014867:Water