Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water

E. M. Kotsalis, I. Hanasaki, Jens Honore Walther, Petros Koumoutsakos

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.
Original languageEnglish
JournalComputers & Mathematics with Applications
Volume59
Pages (from-to)2370-2373
ISSN0898-1221
DOIs
Publication statusPublished - 2010

Cite this

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title = "Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water",
abstract = "We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.",
author = "Kotsalis, {E. M.} and I. Hanasaki and Walther, {Jens Honore} and Petros Koumoutsakos",
year = "2010",
doi = "10.1016/j.camwa.2009.08.054",
language = "English",
volume = "59",
pages = "2370--2373",
journal = "Computers & Mathematics with Applications",
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Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water. / Kotsalis, E. M.; Hanasaki, I.; Walther, Jens Honore; Koumoutsakos, Petros.

In: Computers & Mathematics with Applications, Vol. 59, 2010, p. 2370-2373.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Non-periodic molecular dynamics simulations of coarse grained lipid bilayer in water

AU - Kotsalis, E. M.

AU - Hanasaki, I.

AU - Walther, Jens Honore

AU - Koumoutsakos, Petros

PY - 2010

Y1 - 2010

N2 - We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.

AB - We present a multiscale algorithm that couples coarse grained molecular dynamics (CGMD) with continuum solver. The coupling requires the imposition of non-periodic boundary conditions on the coarse grained Molecular Dynamics which, when not properly enforced, may result in spurious fluctuations of the material properties of the system represented by CGMD. In this paper we extend a control algorithm originally developed for atomistic simulations [3], to conduct simulations involving coarse grained water molecules without periodic boundary conditions. We demonstrate the applicability of our method in simulating more complex systems by performing a non-periodic Molecular Dynamics simulation of a DPPC lipid in liquid coarse grained water.

U2 - 10.1016/j.camwa.2009.08.054

DO - 10.1016/j.camwa.2009.08.054

M3 - Journal article

VL - 59

SP - 2370

EP - 2373

JO - Computers & Mathematics with Applications

JF - Computers & Mathematics with Applications

SN - 0898-1221

ER -