LAMMPS framework for dynamic bonding and an application modeling DNA |
| |
| Authors: | Carsten Svaneborg |
| |
| Affiliation: | 1. Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania;2. Center for Computational Materials Science, Naval Research Laboratory, Washington, D.C.;1. Department of Mechanics and Aerospace Engineering, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, PR China;2. Department of Civil and Environmental Engineering, Shantou University, Shantou, Guangdong, 515063, PR China;3. Intelligent Manufacturing Key Laboratory of Ministry of Education, Shantou University, Shantou, Guangdong, 515063, PR China;4. School of Mechanical Engineering, Shenyang University of Technology, Shenliao West Road No. 111, Shenyang, Liaoning, 110870, PR China;1. US Army Research Laboratory, 4600 Deer Creek Loop, Aberdeen Proving Ground, MD 21005, United States;2. Department of Materials, Polymer Physics, ETH Zürich, CH-8093 Zürich, Switzerland |
| |
| Abstract: | We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion between bond types. Bond formation can be controlled to limit the maximal functionality of a bead with respect to various bond types. Concomitant with the bond dynamics, angular and dihedral interactions are dynamically introduced between newly connected triplets and quartets of beads, where the interaction type is determined from the local pattern of bead and bond types. When breaking bonds, all angular and dihedral interactions involving broken bonds are removed. The framework allows chemical reactions to be modeled, and use it to simulate a simplistic, coarse-grained DNA model. The resulting DNA dynamics illustrates the power of the present framework.Program summaryProgram title: LAMMPS Framework for Directional Dynamic BondingCatalogue identifier: AEME_v1_0Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEME_v1_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: GNU General Public LicenceNo. of lines in distributed program, including test data, etc.: 2 243 491No. of bytes in distributed program, including test data, etc.: 771Distribution format: tar.gzProgramming language: C++Computer: Single and multiple core serversOperating system: Linux/Unix/WindowsHas the code been vectorized or parallelized?: Yes. The code has been parallelized by the use of MPI directives.RAM: 1 GbClassification: 16.11, 16.12Nature of problem: Simulating coarse-grain models capable of chemistry e.g. DNA hybridization dynamics.Solution method: Extending LAMMPS to handle dynamic bonding and directional bonds.Unusual features: Allows bonds to be created and broken while angular and dihedral interactions are kept consistent.Additional comments: The distribution file for this program is approximately 36 Mbytes and therefore is not delivered directly when download or E-mail is requested. Instead an html file giving details of how the program can be obtained is sent.Running time: Hours to days. The examples provided in the distribution take just seconds to run. |
| |
| Keywords: | |
| 本文献已被 ScienceDirect 等数据库收录！ |
|
