Premium
Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water
Author(s) -
Kitchen Douglas B.,
Hirata Fumio,
Westbrook John D.,
Levy Ronald,
Kofke David,
Yarmush Martin
Publication year - 1990
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540111009
Subject(s) - verlet integration , smoothing , molecular dynamics , cutoff , classification of discontinuities , statistical physics , chemistry , equations of motion , thermodynamic integration , internal energy , function (biology) , biological system , physics , computational chemistry , classical mechanics , thermodynamics , computer science , mathematics , mathematical analysis , quantum mechanics , evolutionary biology , biology , computer vision
Abstract Molecular dynamics simulations have been carried out for a series of systems of increasing complexity including: pure water, a model polypeptide (α‐helical decaglycine) in vacuo, a protein (Pancreatic Trypsin Inhibitor, PTI) in vacuo, and a fully solvated protein (PTI in water). The equations of motion were integrated using Andersen's velocity version of the Verlet algorithm with internal contraints (the RATTLE algorithm). The accuracy with which the equations of motion are integrated has been analyzed for several different simulation conditions. The effects of various nonbonded interaction truncation schemes on the conservation of energy have been examined, including the use of atomic cutoffs, and (neutral group) residue cutoffs. The use of a smoothing function to eliminate the discontinuities in the potential at the cutoff leads to a significant improvement in the accuracy of the integration for each of the systems studied. The accuracy with which the equations of motion are integrated using the RATTLE algorithm for pure water and for the solvated protein are found to be comparable when the nonbonded interactions are tapered with a smoothing function at the cutoff.