title: On easy implementation of a variant of the replica exchange with solute tempering in GROMACS.
abstract: To reduce the number of replicas required in the conventional replica exchange method for huge systems, recently the replica exchange with solute tempering (REST) method was proposed. Here we showed that a variant of REST realized by rescaling the force-field parameters can be performed with GROMACS 4 without changing the code. We tested the variant REST for alanine dipeptide and an N-terminal peptide from p53 confirming its performance nearly equal to the original REST.
authors.affiliation: Department of Biophysics Graduate School of Science, Kyoto University, Kyoto, Japan.
authors.forename: Tsuyoshi
authors.initials: T
authors.lastname: Terakawa
authors.forename: Tomoshi
authors.initials: T
authors.lastname: Kameda
authors.forename: Shoji
authors.initials: S
authors.lastname: Takada
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000465:Algorithms; D004151:Dipeptides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D012995:Solubility
chemical_list: D004151:Dipeptides; D000409:Alanine