TY - JOUR
T1 - Microsecond Molecular Dynamics Simulations of Proteins Using a Quasi-Equilibrium Solvation Shell Model
AU - Ovchinnikov, Victor
AU - Conti, Simone
AU - Lau, Edmond Y.
AU - Lightstone, Felice C.
AU - Karplus, Martin
PY - 2020/3/10
Y1 - 2020/3/10
N2 - We describe the development and implementation of a quasi-equilibrium hydration shell model of biomolecular solvation with adaptive boundaries. Applying the model to microsecond-long molecular dynamics simulations of several protein systems of varying complexity, we find that the model simulation results are of comparable quality to those obtained from simulations of fully solvated systems, but at a reduced computational cost. We discuss the dominant sources of error in the model and outline directions for future improvements.
AB - We describe the development and implementation of a quasi-equilibrium hydration shell model of biomolecular solvation with adaptive boundaries. Applying the model to microsecond-long molecular dynamics simulations of several protein systems of varying complexity, we find that the model simulation results are of comparable quality to those obtained from simulations of fully solvated systems, but at a reduced computational cost. We discuss the dominant sources of error in the model and outline directions for future improvements.
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U2 - 10.1021/acs.jctc.9b01072
DO - 10.1021/acs.jctc.9b01072
M3 - Article
C2 - 32045240
AN - SCOPUS:85081941253
VL - 16
SP - 1866
EP - 1881
JO - Journal of Chemical Theory and Computation
JF - Journal of Chemical Theory and Computation
SN - 1549-9618
IS - 3
ER -