| POLYMERS Vol.64 No.3 |
| >> Japanese | >> English |
COVER STORY
Useful Software for the Calculation of Macromolecules in Your Lab |
| COVER STORY: Tutorial |
| What You Should Consider before Starting Simulation of Macromolecules | Masako TAKASU |
| <Abstract> In this tutorial article, we explain what you should consider before performing computer simulation of macromolecules. The choice of software depends on what you want to simulate and the length scale you would like to focus on. It is a good idea to find someone near your office who can teach you how to use the software. For busy professors at universities, it might be better to find a graduate student who can work on the calculations instead of doing everything by yourself. The books which will help you understand the theory behind the software are introduced at the end of the article. Keywords: Software / Computer / Macromolecules / Simulation / Physics / Molecular Dynamics / Equation of Motion |
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| COVER STORY: Highlight Reviews |
| OCTA (Integrated Simulator for Soft Materials) | Takashi HONDA |
| <Abstract> OCTA is an integrated simulation system developed by a national project in Japan for soft materials. OCTA introduced the concept of multi-scale and multi-physics in an early stage and focuses to the simulations in the meso-region. For example, an ABA triblock polymer was used as a model of a thermoplastic elastomer and a multiscale simultaion was done by the OCTA to show it's feature. Keywords: OCTA / COGANC / SUSHI / Coarse-Grained MD / SCF Theory / Multi-Scale / Multi-Physics / Thermoplastic Elastomer |
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| Introduction of LAMMPS for Polymer Physics | Katsumi HAGITA |
| <Abstract> LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator) is the most used Open Source Software (OSS) to study mechanial properties with molecular dynamics simulations in the field of polymer, carbon and metal materials. The LAMMPS is developed and mainteined by Sandia National Laboratory, USA. The author considers the advantages of LAMMPS for beginners to be the simple input-output files with text format, seamless from single PC computing to massively parallel computing and easiness of modification of program codes. The LAMMPS is also widely used by Japanese researchers. The author gives an introductions for beginners and showcases results and examples by several Japanese researchers. Keywords: Molecular Dynamics Simulation / LAMMPS / Bead-Spring Model / Coarse Grained Model |
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| GROMACS and Its Application to Coordination Polymers | Makoto YONEYA |
| <Abstract> The molecular dynamics simulation software, GROMACS, is explained. Simulation of a coordination polymer network is introduced as an application example of GROMACS. Keywords: GROMACS / Molecular Dynamics Simulation / Self-Assembly / Coordination Polymer / Metal-Origanic Framework / Coordination Interaction / Implicit Solvent |
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| Molecular Dynamics Simulation for Protein Systems by NAMD | Hiroaki SAITO |
| <Abstract> NAMD is a molecular dynamics code designed for high-performance simulation of biomolecular systems. In this manuscript, I present a brief introduction of the MD simulation of small protein systems for beginners. The preparations to conduct the MD simulation and brief analysis examples are also presented. Keywords: NAMD / VMD / Protein / Molecular Dynamids |
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| Introduction to Molecular Modeling with Gaussinan | Kimikazu SUGIMORI |
| <Abstract> The author summarizes the procedure of molecular modeling with the quantum chemical calculation software, Gaussian. Actual calculations by using molecular orbital theory and density functional theory, and cautionary notes are also provided. Keywords: Molecular Orbital / Density Functional Theory / Gaussian |
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| Polymer Science and I: A Personal Account |
| Education has a Way of Repeating Itself | Kanjiro MIYATA |
| <Abstract> This article describes the author's own experience of writing pubrication papers, particularly highlighliting the communication with his supervisor. |
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| Front-Line Polymer Science |
| Predicting Polymer Rheology by Slip-Link Model | Jun-ichi TAKIMOTO |
| <Abstract> Entanglements among polymer chains can be modeled by slip-links (two polymer chains passing through a virtual ring), with the assumption that the entanglement is a binary interaction, i.e., exactly two chains are always involved. The model can take account of the three most important relaxation mechanisms in entangled polymeric liquids; reptation, contour length fluctuation (CLF) and constraint release (CR). Simulations using the slip-link model can successfully predict various linear and nonlinear rheological properties of linear and star polymer melts. Polydispersity can also be easily taken account of. Especially, strong enhancement of the stain hardening of uniaxial elongational viscosity by a small amount of ultra high molecular weight component can be quantitatively predicted without any adjustable parameter. Keywords: Entanglement / Slip-Link / Constraint Release / Conour Length Fluctuation / Reptation / Elongational Viscosity / Strain Hardening |
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