Substructured multibody molecular dynamics.

TLDR: New features of the LAMMPS software package are used to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface, and motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

Abstract: We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov) to include many new features for accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes of MD for practitioners and researchers in numerical analysis and computational mechanics.

Figures

Figure 9. Images153 of the rhodopsin protein, Lys 296 (retinal) with Glu 113 and Cys 187, and nearby waters at different times a) t = 64 ns, b) t = 65 ns, c) t = 66 ns and d) t = 67 ns. Helices 3 (orange) and 7 (cyan) are also visible in a cartoon representation. Lys 296 is on Helix 7 and Glu 113 is on Helix 3.

Figure 4. Kink angles as a function of time for Helices 5b-5c (kink at His 211) and 6a-6b (kink at Pro 267).

TABLE VI: Comparison of surface tension for the SPC/E model as a function of calculation method.

TABLE V: Surface tension for the SPC/E model as a function of LJ cutoff.

Figure 1. Sample simulation cell, showing equilibrated configurations of 1000 SPC/E water molecules at (a) 300 K and (b) 500 K . The dimensions of the cell are 2 3 nmx yL L L= = = . and 13 5 nmzL L⊥= = . .

Figure 5. Interaction energies between retinal’s beta ionone ring and nearby side chains.

Full text

SANDIA REPORT
SAND 2006-7085
Unlimited Release
Printed November 2006
Substructured Multibody Molecular
Dynamics
Paul S. Crozier, Andrei I. Drăgănescu, Gary S. Grest, Ahmed E. Ismail,
Richard B. Lehoucq, Rudranarayan M. Mukherjee, Steven J. Plimpton,
Mark J. Stevens, and Thomas B. Woolf
Prepared by
Sandia National Laboratories
Albuquerque, New Mexico 87185 and Livermore, California 94550
Sandia is a multiprogram laboratory operated by Sandia Corporation,
a Lockheed Martin Company, for the United States Department of Energy’s
National Nuclear Security Administration under Contract DE-AC04-94AL85000.
Approved for public release; further dissemination unlimited.

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SAND 2006-7085
Unlimited Release
Printed November 2006
Substructured Multibody Molecular Dynamics
Paul S. Crozier
Multiscale Computational Materials Methods
Andrei I. Drăgănescu and Richard B. Lehoucq
Computational Math/Algorithms
Gary S. Grest
Surface & Interface Sciences
Ahmed E. Ismail
Perf. Assmt. & Dec. Anal.
Steven J. Plimpton
Computational Biology
Mark J. Stevens
Biomolecular Analys & Imaging
Sandia National Laboratories
P.O. Box 5800
Albuquerque, NM 87185
Rudranarayan M. Mukherjee
Department of M.A.N.E.
Rensselaer Polytechnic Institute
Troy, New York 12180
Thomas B. Woolf
Johns Hopkins University
School of Medicine
Baltimore, Maryland 21205
Abstract
We have enhanced our parallel molecular dynamics (MD) simulation software LAMMPS (Large-scale
Atomic/Molecular Massively Parallel Simulator, lammps.sandia.gov
) to include many new features for
accelerated simulation including articulated rigid body dynamics via coupling to the Rensselaer
Polytechnic Institute code POEMS (Parallelizable Open-source Efficient Multibody Software). We use
new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water
model surface tension and capillary waves at the vapor-liquid interface. Finally, we motivate the recipes
of MD for practitioners and researchers in numerical analysis and computational mechanics.

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Contents
Contents 5
Chapter 1: Substructured molecular dynamics simulations using multibody dynamics
algorithms through LAMMPS-POEMS coupling 7
Abstract 7
1. Introduction 7
2. Modeling Approach 8
2.1 Kinematic Model 8
2.2. Generating the rigid body properties 10
3. Algorithm Overview 10
3.1. Mathematical Preliminaries 11
4. ()On Forward Dynamics Analysis 12
4.1. Recursive Kinematic Relationships 12
4.2. Triangularization 13
4.3. Back-Substitutions 14
5. Time Integration 14
6. Applications and Results 15
6.1. Water Box 15
6.2. Alanine Dipeptide 15
6.3. DNA simulations 16
6.4. Box of alkanes 16
6.5. C-Terminal of Ribosomal 16
6.6. C-Terminal of Rubisco 16
6.7. Rhodopsin 17
7. Software Development 17
8. Conclusions 19
Acknowledgments 19
References 20
Chapter 2: How a small change in retinal leads to G-protein activation: initial events
suggested by molecular dynamics calculations 21
Abstract 21
Introduction 21
Simulation method 22
Results 23
C11-C12 dihedral transition 23
Retinal – Ala 169 gap narrows 24
Helix tilt and kink angle transitions 24
PSB counterion switch 26
C3 loop 27
Large-scale structural changes 27
Discussion 27
Conclusions 33
Table I 35
Figures 36
References 46

Frequently asked questions

Q1. What are the contributions in "Substructured multibody molecular dynamics" ?

The authors use new features of the LAMMPS software package to investigate rhodopsin photoisomerization, and water model surface tension and capillary waves at the vapor-liquid interface. 

Q2. What are the future works in "Substructured multibody molecular dynamics" ?

The authors have demonstrated that examining capillary waves at the liquid-vapor interface can be used to determine the surface tension of real fluids, and that the use of an error function profile offers better results in comparison to experimental data than the use of a hyperbolic tangent profile.