Optimal allocation of replicas in parallel tempering simulations.
We have studied the efficiency of parallel tempering simulations for a variety of systems including a coarse-grained protein, an atomistic model polypeptide, and the Lennard-Jones fluid. A scheme is proposed for the optimal allocation of temperatures in these simulations. The method is compared to the existing empirical approaches used for this purpose. Accuracy associated with the computed thermodynamic quantities such as specific heat is also computed and their dependence on the trial-exchange acceptance rate is reported.
Rathore
Nitin
N
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
Chopra
Manan
M
de Pablo
Juan J
JJ
D001426:Bacterial Proteins / Q000737:chemistry; D003198:Computer Simulation; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017434:Protein Structure, Tertiary; D013205:Staphylococcal Protein A / Q000737:chemistry*; D013696:Temperature
D001426:Bacterial Proteins; C034284:IgG Fc-binding protein, Streptococcus; D010455:Peptides; D013205:Staphylococcal Protein A; C019529:polyalanine