Replica exchange simulation method using temperature and solvent viscosity.
We propose an efficient and simple method for fast conformational sampling by introducing the solvent viscosity as a parameter to the conventional temperature replica exchange molecular dynamics (T-REMD) simulation method. The method, named V-REMD (V stands for viscosity), uses both low solvent viscosity and high temperature to enhance sampling for each replica; therefore it requires fewer replicas than the T-REMD method. To reduce the solvent viscosity by a factor of lambda in a molecular dynamics simulation, one can simply reduce the mass of solvent molecules by a factor of lambda(2). This makes the method as simple as the conventional method. Moreover, thermodynamic and conformational properties of structures in replicas are still useful as long as one has sufficiently sampled the Boltzmann ensemble. The advantage of the present method has been demonstrated with the simulations of the trialanine, deca-alanine, and a 16-residue beta-hairpin peptides. It shows that the method could reduce the number of replicas by a factor of 1.5 to 2 as compared with the T-REMD method.
Nguyen
Phuong H
PH
Institute of Physical and Theoretical Chemistry, J. W. Goethe University, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany. phuong@theochem.uni-frankfurt.de
D000409:Alanine / Q000737:chemistry; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry; D010455:Peptides / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D013696:Temperature; D013816:Thermodynamics; D014783:Viscosity
D009842:Oligopeptides; D010455:Peptides; D012997:Solvents; C039944:alanyl-alanyl-alanine; D000409:Alanine