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Partial rigid‐body dynamics in NPT, NPAT and NPγT ensembles for proteins and membranes
Author(s) -
Ikeguchi Mitsunori
Publication year - 2004
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.10402
Subject(s) - molecular dynamics , membrane , rigid body , chemistry , computation , integrator , constant (computer programming) , symplectic geometry , computational chemistry , classical mechanics , statistical physics , physics , mathematical analysis , mathematics , algorithm , computer science , quantum mechanics , biochemistry , voltage , programming language
A partial rigid‐body method of molecular dynamics simulations for proteins and membranes is presented. In this method, the symplectic integrator for rigid bodies is combined with the equations of motion for the NPT ensemble. The standard NPT ensemble is extended to the membrane‐specific ensembles, the NPAT (constant normal pressure and lateral surface area of membranes and constant temperature) and NPγT (constant normal pressure and lateral surface tension of membranes and constant temperature) ensembles. By more than 30‐ns simulations of aqueous proteins and hydrated lipid bilayers, the results of the partial rigid‐body method demonstrated excellent conservation of total energy and consistent behavior with the traditional constraint method in terms of structural distribution and fluctuation of proteins and lipids. The efficient implementation of the partial rigid‐body method in parallel computation is presented, which is shown to work well in large‐scale molecular dynamics simulations. © 2004 Wiley Periodicals, Inc. J Comput Chem 25: 529–541, 2004