The temperature intervals with global exchange of replicas empirical accelerated sampling method: parameter sensitivity and extension to a complex molecular system.
The recently developed "temperature intervals with global exchange of replicas" (TIGER2) algorithm is an efficient replica-exchange sampling algorithm that provides the freedom to specify the number of replicas and temperature levels independently of the size of the system and temperature range to be spanned, thus making it particularly well suited for sampling molecular systems that are considered to be too large to be sampled using conventional replica exchange methods. Although the TIGER2 method is empirical in nature, when appropriately applied it is able to provide sampling that satisfies the balance condition and closely approximates a Boltzmann-weighted ensemble of states. In this work, we evaluated the influence of factors such as temperature range, temperature spacing, replica number, and sampling cycle design on the accuracy of a TIGER2 simulation based on molecular dynamics simulations of alanine dipeptide in implicit solvent. The influence of these factors is further examined by calculating the properties of a complex system composed of the B1 immunoglobulin-binding domain of streptococcal protein G (protein G) in aqueous solution. The accuracy of a TIGER2 simulation is particularly sensitive to the maximum temperature level selected for the simulation. A method to determine the appropriate maximum temperature level to be used in a TIGER2 simulation is presented.
Li
Xianfeng
X
Department of Bioengineering, Clemson University, Clemson, South Carolina 29634, USA.
Latour
Robert A
RA
D000409:Alanine / Q000031:analogs & derivatives / Q000737:chemistry*; D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry*; D004151:Dipeptides / Q000737:chemistry*; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D013696:Temperature
D001426:Bacterial Proteins; D004151:Dipeptides; C034284:IgG Fc-binding protein, Streptococcus; D000409:Alanine