LAMMPS framework for dynamic bonding and an application modeling DNA

详细信息	查看全文 | 推荐本文 |

• 作者：Carsten Svaneborg ^{science@zqex.dk}
• 关键词：Dynamic directional bonds ; Coarse-grain DNA models ; Chemical reactions ; Molecular and dissipative particle dynamics
• 刊名：Computer Physics Communications
• 出版年：2012
• 期刊代码：30_00104655
• 类别：cp
• 出版时间：August, 2012
• 卷：183
• 期：8
• 页码：1793-1802
• 文件大小：1354 K

摘要

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 summary

Program title: LAMMPS Framework for Directional Dynamic Bonding

Catalogue identifier: AEME_v1_0

Program summary URL:

Program obtainable from: CPC Program Library, Queen始s University, Belfast, N. Ireland

Licensing provisions: GNU General Public Licence

No. of lines in distributed program, including test data, etc.: 2鈥?43鈥?91

No. of bytes in distributed program, including test data, etc.: 771

Distribution format: tar.gz

Programming language: C++

Computer: Single and multiple core servers

Operating system: Linux/Unix/Windows

Has the code been vectorized or parallelized?: Yes. The code has been parallelized by the use of MPI directives.

RAM: 1 Gb

Classification: 16.11, 16.12

Nature 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.