POLYANA—A tool for the calculation of molecular radial distribution functions based on Molecular Dynamics trajectories

详细信息    查看全文

• 作者：Christos Dimitroulis^a ; Theophanes Raptis^a ; Vasilios Raptis^b ; ^{v.raptis@inn.demokritos.gr" class="auth_mail" title="E-mail the corresponding author}
• 关键词：Computer simulation of liquid structure ; Molecular Dynamics simulations ; Radial distribution functions ; DL_POLY
• 刊名：Computer Physics Communications
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：197
• 期：Complete
• 页码：220-226
• 全文大小：466 K

文摘

We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to ‘hack’ the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.

Program summary

Program title: Polyana

Catalogue identifier: AEXP_v1_0

Program summary URL:ype="url" data-locatorKey="http://cpc.cs.qub.ac.uk/summaries/AEXP_v1_0.html">http://cpc.cs.qub.ac.uk/summaries/AEXP_v1_0.html

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

Licensing provisions: MIT License

No. of lines in distributed program, including test data, etc.: 33638

No. of bytes in distributed program, including test data, etc.: 574799

Distribution format: tar.gz

Programming language: Fortran.

Computer: Any computer that can run a Fortran compiler.

Operating system: Tested on CentOS 6.6, Ubuntu 12.04 and Ubuntu 15.04.

RAM: Proportional to the size of the simulated system (number of atoms).

Classification: 4.14, 7.7.

Nature of problem: Computation of radial distribution functions of molecular centres of mass in systems subjected to Periodic Boundary Conditions.

Solution method: Molecules of arbitrary topology are ‘unfolded’ using a generic algorithm and their centres of mass are computed; then, standard procedures are applied.

Additional comments: The code has been designed with ease of use in mind; in most cases, no user input will be required, except the simulation input/output files.

Abbreviations: RDF: Radial Distribution Function PBC: Periodic Boundary Conditions

Running time: Of the order of seconds to minutes, depending on platform and simulation size.