MOLSIM: A modular molecular simulation software.
MOLSIM: A modular molecular simulation software.
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DOI：
10.1002/jcc.23919
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发表时间：
2015-06-15
影响因子：
3
通讯作者：
Linse, Per
中科院分区：
文献类型：
--
作者：
Rescic, Jurij;Linse, Per
关键词：
介绍了用于全原子分子和粗粒度模拟的模块化软件MOLSIM，重点介绍了所使用的基本概念。该软件具有四个独特的特点：（1）它是一个集成的软件，分子动力学，蒙特卡罗和布朗动力学模拟;（2）模拟对象以分层的方式构建，代表原子，刚性分子和胶体，柔性链，分层聚合物和交联网络;（3）涉及电荷、偶极子和/或各向异性偶极子极化率的长程相互作用可以用标准埃瓦尔德求和、光滑粒子网格埃瓦尔德求和或反应场技术来处理;（4）对所有计算的观测量提供统计不确定性。此外，MOLSIM支持各种统计集成，并提供多种类型的模拟单元和边界条件。分子间相互作用包括表列的速度和均匀性的成对势，多体相互作用涉及各向异性极化率。分子内相互作用包括键、角和交联势。一个非常大的静态和动态性能的分析。MOLSIM的功能可以通过用户提供的控制程序来扩展，例如，启动条件、分子间电位和分析。软物质领域的一组广泛的案例研究，包括胶体，聚合物和交联网络。版权所有© 2015作者.计算化学杂志由Wiley Periodicals，Inc.出版。
The modular software MOLSIM for all‐atom molecular and coarse‐grained simulations is presented with focus on the underlying concepts used. The software possesses four unique features: (1) it is an integrated software for molecular dynamic, Monte Carlo, and Brownian dynamics simulations; (2) simulated objects are constructed in a hierarchical fashion representing atoms, rigid molecules and colloids, flexible chains, hierarchical polymers, and cross‐linked networks; (3) long‐range interactions involving charges, dipoles and/or anisotropic dipole polarizabilities are handled either with the standard Ewald sum, the smooth particle mesh Ewald sum, or the reaction‐field technique; (4) statistical uncertainties are provided for all calculated observables. In addition, MOLSIM supports various statistical ensembles, and several types of simulation cells and boundary conditions are available. Intermolecular interactions comprise tabulated pairwise potentials for speed and uniformity and many‐body interactions involve anisotropic polarizabilities. Intramolecular interactions include bond, angle, and crosslink potentials. A very large set of analyses of static and dynamic properties is provided. The capability of MOLSIM can be extended by user‐providing routines controlling, for example, start conditions, intermolecular potentials, and analyses. An extensive set of case studies in the field of soft matter is presented covering colloids, polymers, and crosslinked networks. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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影响因子：
3.4
作者：
Abrikosov, Alexei I.;Sacanna, Stefano;Linse, Per
通讯作者：
Linse, Per
影响因子：
3.9
作者：
Akinchina, Anna;Linse, Per
通讯作者：
Linse, Per
影响因子：
1.6
作者：
Linse, Per;Karlstrom, Gunnar
通讯作者：
Karlstrom, Gunnar
影响因子：
4.4
作者：
ESSMANN, U;PERERA, L;PEDERSEN, LG
通讯作者：
PEDERSEN, LG
影响因子：
15
作者：
LINSE, P
通讯作者：
LINSE, P