MBO(N)D: A multibody method for long-time molecular dynamics simulations

H M Chun; C E Padilla; D N Chin; M Watanabe; V I Karlov; H E Alper; K Soosaar; K B Blair; O M Becker; L S D Caves; R Nagle; D N Haney; B L Farmer

MBO(N)D: A multibody method for long-time molecular dynamics simulations

H M Chun, C E Padilla, D N Chin, M Watanabe, V I Karlov, H E Alper, K Soosaar, K B Blair, O M Becker, L S D Caves, R Nagle, D N Haney, B L Farmer

Biology

Research output: Contribution to journal › Literature review › peer-review

Abstract

A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body-based modes. This approach allows for the elimination of the high-frequency harmonic motion while capturing the low-frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5- to 30-fold over atomistic simulations have been realized in various applications of the method. (C) 2000 John Wiley & Sons, Inc.

Original language	English
Pages (from-to)	159-184
Number of pages	26
Journal	Journal of computational chemistry
Volume	21
Issue number	3
Publication status	Published - Feb 2000

Keywords

molecular dynamics
normal modes
anharmonicity
macromolecules
numerical integrators
PANCREATIC TRYPSIN-INHIBITOR
PRINCIPAL COMPONENT ANALYSIS
L7/L12 RIBOSOMAL-PROTEIN
FREQUENCY NORMAL-MODES
ATOMIC FLUCTUATIONS
COLLECTIVE MOTIONS
STEP METHODS
TERMINAL FRAGMENT
AQUEOUS-SOLUTION
HIV-1 PROTEASE

Cite this

@article{ba969f83f20c4820a2b8e1732dd67df5,

title = "MBO(N)D: A multibody method for long-time molecular dynamics simulations",

abstract = "A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body-based modes. This approach allows for the elimination of the high-frequency harmonic motion while capturing the low-frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5- to 30-fold over atomistic simulations have been realized in various applications of the method. (C) 2000 John Wiley & Sons, Inc.",

keywords = "molecular dynamics, normal modes, anharmonicity, macromolecules, numerical integrators, PANCREATIC TRYPSIN-INHIBITOR, PRINCIPAL COMPONENT ANALYSIS, L7/L12 RIBOSOMAL-PROTEIN, FREQUENCY NORMAL-MODES, ATOMIC FLUCTUATIONS, COLLECTIVE MOTIONS, STEP METHODS, TERMINAL FRAGMENT, AQUEOUS-SOLUTION, HIV-1 PROTEASE",

author = "Chun, {H M} and Padilla, {C E} and Chin, {D N} and M Watanabe and Karlov, {V I} and Alper, {H E} and K Soosaar and Blair, {K B} and Becker, {O M} and Caves, {L S D} and R Nagle and Haney, {D N} and Farmer, {B L}",

year = "2000",

month = feb,

language = "English",

volume = "21",

pages = "159--184",

journal = "Journal of computational chemistry",

issn = "0192-8651",

publisher = "Wiley-Blackwell",

number = "3",

}

TY - JOUR

T1 - MBO(N)D: A multibody method for long-time molecular dynamics simulations

AU - Chun, H M

AU - Padilla, C E

AU - Chin, D N

AU - Watanabe, M

AU - Karlov, V I

AU - Alper, H E

AU - Soosaar, K

AU - Blair, K B

AU - Becker, O M

AU - Caves, L S D

AU - Nagle, R

AU - Haney, D N

AU - Farmer, B L

PY - 2000/2

Y1 - 2000/2

N2 - A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body-based modes. This approach allows for the elimination of the high-frequency harmonic motion while capturing the low-frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5- to 30-fold over atomistic simulations have been realized in various applications of the method. (C) 2000 John Wiley & Sons, Inc.

AB - A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body-based modes. This approach allows for the elimination of the high-frequency harmonic motion while capturing the low-frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5- to 30-fold over atomistic simulations have been realized in various applications of the method. (C) 2000 John Wiley & Sons, Inc.

KW - molecular dynamics

KW - normal modes

KW - anharmonicity

KW - macromolecules

KW - numerical integrators

KW - PANCREATIC TRYPSIN-INHIBITOR

KW - PRINCIPAL COMPONENT ANALYSIS

KW - L7/L12 RIBOSOMAL-PROTEIN

KW - FREQUENCY NORMAL-MODES

KW - ATOMIC FLUCTUATIONS

KW - COLLECTIVE MOTIONS

KW - STEP METHODS

KW - TERMINAL FRAGMENT

KW - AQUEOUS-SOLUTION

KW - HIV-1 PROTEASE

M3 - Literature review

SN - 0192-8651

VL - 21

SP - 159

EP - 184

JO - Journal of computational chemistry

JF - Journal of computational chemistry

IS - 3

ER -