Generalized essential energy space random walks to more effectively accelerate solute sampling in aqueous environment.
Molecular dynamics sampling can be enhanced via the promoting of potential energy fluctuations, for instance, based on a Hamiltonian modified with the addition of a potential-energy-dependent biasing term. To overcome the diffusion sampling issue, which reveals the fact that enlargement of event-irrelevant energy fluctuations may abolish sampling efficiency, the essential energy space random walk (EESRW) approach was proposed earlier. To more effectively accelerate the sampling of solute conformations in aqueous environment, in the current work, we generalized the EESRW method to a two-dimension-EESRW (2D-EESRW) strategy. Specifically, the essential internal energy component of a focused region and the essential interaction energy component between the focused region and the environmental region are employed to define the two-dimensional essential energy space. This proposal is motivated by the general observation that in different conformational events, the two essential energy components have distinctive interplays. Model studies on the alanine dipeptide and the aspartate-arginine peptide demonstrate sampling improvement over the original one-dimension-EESRW strategy; with the same biasing level, the present generalization allows more effective acceleration of the sampling of conformational transitions in aqueous solution. The 2D-EESRW generalization is readily extended to higher dimension schemes and employed in more advanced enhanced-sampling schemes, such as the recent orthogonal space random walk method.
Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA.
Chao
C
Lv
Lianqing
L
Zheng
Wei
W
Yang
D000409:Alanine / Q000737:chemistry*; D001224:Aspartic Acid / Q000737:chemistry*; D004151:Dipeptides / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D012996:Solutions; D014867:Water / Q000737:chemistry*
D004151:Dipeptides; D012996:Solutions; D014867:Water; D001224:Aspartic Acid; D000409:Alanine