A selective integrated tempering method.
In this paper, based on the integrated tempering sampling we introduce a selective integrated tempering sampling (SITS) method for the efficient conformation sampling and thermodynamics calculations for a subsystem in a large one, such as biomolecules solvated in aqueous solutions. By introducing a potential surface scaled with temperature, the sampling over the configuration space of interest (e.g., the solvated biomolecule) is selectively enhanced but the rest of the system (e.g., the solvent) stays largely unperturbed. The applications of this method to biomolecular systems allow highly efficient sampling over both energy and configuration spaces of interest. Comparing to the popular and powerful replica exchange molecular dynamics (REMD), the method presented in this paper is significantly more efficient in yielding relevant thermodynamics quantities (such as the potential of mean force for biomolecular conformational changes in aqueous solutions). It is more important that SITS but not REMD yielded results that are consistent with the traditional umbrella sampling free energy calculations when explicit solvent model is used since SITS avoids the sampling of the irrelevant phase space (such as the boiling water at high temperatures).
Yang
Lijiang
L
Department of Chemistry, Texas A&M University, College Station, Texas 77843, USA.
Qin Gao
Yi
Y
D000595:Amino Acid Sequence; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D004187:Disaccharides / Q000737:chemistry*; D008956:Models, Chemical; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D004151:Dipeptides; D004187:Disaccharides; D011506:Proteins; C483378:methylmaltoside; D014867:Water; C002956:alanylalanine