TIGER2: an improved algorithm for temperature intervals with global exchange of replicas.
An empirical sampling method for molecular simulation based on "temperature intervals with global exchange of replicas" (TIGER2) has been developed to reduce the high demand for computational resources and the low computational efficiency of the conventional replica-exchange molecular dynamics (REMD) method. This new method overcomes the limitation of its previous version, called TIGER, which requires the assumption of constant heat capacity during quenching of replicas from elevated temperatures to the baseline temperature. The robustness of the TIGER2 method is examined by comparing it against a Metropolis Monte Carlo simulation for sampling the conformational distribution of a single butane molecule in vacuum, a REMD simulation for sampling the behavior of alanine dipeptide in explicit solvent, and REMD simulations for sampling the folding behavior of two peptides, (AAQAA)(3) and chignolin, in implicit solvent. The agreement between the results from these conventional sampling methods and the TIGER2 simulations indicates that the TIGER2 algorithm is able to closely approximate a Boltzmann-weighted ensemble of states for these systems but without the limiting assumptions that were required for the original TIGER algorithm. TIGER2 is an efficient replica-exchange sampling method that enables the number of replicas that are used for a replica-exchange simulation to be substantially reduced compared to the conventional REMD method.
Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, USA.
Xianfeng
X
Li
Robert A
RA
Latour
Steven J
SJ
Stuart
D000409:Alanine / Q000737:chemistry; D000465:Algorithms; D000595:Amino Acid Sequence; D002073:Butanes / Q000737:chemistry; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry; D008958:Models, Molecular; D009010:Monte Carlo Method; D009842:Oligopeptides / Q000737:chemistry; D011487:Protein Conformation; D012997:Solvents / Q000737:chemistry; D013696:Temperature
D002073:Butanes; D004151:Dipeptides; D009842:Oligopeptides; D012997:Solvents; C506175:chignolin; C046888:butane; D000409:Alanine