MOLSIM: A modular molecular simulation software

Abstract

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.

Keywords: Brownian dynamics; Ewald sum; Monte Carlo simulation; all-atom model; boundary conditions; coarse-grained model; ensembles; molecular dynamics; molecular simulation; software.

Figure 1

Illustration of three protocols of performing a simulation. The protocols are further discussed in the text. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Figure 2

Illustration of the concepts task, subtask, and stage of a simple simulation software. Here, three stages, separated by dotted lines, and three tasks given in frames of different color are present. Task b) is divided into three subtasks. Moreover, task a) appears in stage 1), task b) appears in all three stages, and task c) appears in stage 2). [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Figure 3

Illustration of different boundary conditions: a) parallelepiped with periodic boundary conditions (pbc:s) in all three directions, b) parallelepiped with pbc:s in the x and y directions, c) parallelepiped with pbc in the z direction, d) cylindrical boundary conditions, e) ellipsoidal boundary conditions, and f) spherical boundary condition. The gray areas represent impenetrable surfaces. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Figure 4

Illustration of the objects (i) atom, (ii) particle, (iii) chain, and (iv) hierarchical structure and their relations. Here, the atom possesses the hard‐core radius R, charge q (dark blue), and dipole moment m (red); the particle is composed of three atoms of two different types (yellow and light green) positioned in a local coordinate system (x′y′z′); the chain is composed of four particles of two different types (green and orange); and finally the hierarchical structure is made of chains of four different types (green, orange, purple, and blue). [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Figure 5

Illustration of nonbonded potential acting between atoms (filled circles) and bond, angle, and crosslink potential acting among particles (open circles). [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Figure 6

Illustration of a system (blue), which possesses an inscribed insertion box (red), which in turn is divided into (right) unit cells, in which particles are positioned. The insertion boxes and unit cells are always described by parallelepipeds. Here, the unit cell possesses two particles in a body‐centered cubic symmetry. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Figure 7

Illustration of data flow of the software MOLSIM controlled by files. Data always read and written are given by thick arrows. Flow of data first generated and written and later analyzed are given by dashed lines. FIN refers to the input file, FCNF to the configuration file, FLIB to a library file containing parameters of interaction potentials, FOUT to the output file, FLIST to the list file, FIMG to the image file, FUSER to a file used by the user‐provided code, FGROUP to the group file, and FDUMP to the set of dump files. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Figure 8

Illustration of the parallelization protocol for reading and CPU‐intensive operations. a) Section of parallel computation involving nonintensive operations (gray) executed on all nodes followed by CPU intensive operations distributed among all nodes (blue) and communication (red). b) Reading section involving nonintensive operations (gray) executed on all nodes followed by reading of input by the master only (green) and communication of values of input variables (red). [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Figure 9

Illustration of dipolar systems investigated comprising a) examination of the influence of the Ewald sum boundary condition of dipolar fluids and b) a study of ordering in dipolar fluids when the shape or the interaction of the spherical dipoles are perturbed. Key references: a) Refs. [23, 24] and b) [25, 26]. a) Reprinted with permission from J. Chem. Phys. 2009, 131, 164507. Copyright 2009, AIP Publishing LLC. b) Reprinted with permission from J. Stat. Phys. 2011, 145, 418–440.

Figure 10

Illustration of colloidal systems comprising a) examination of a new and rapid algorithm for dealing with dielectric discontinuities in spherical geometry, b) charged colloidal solution including the limit of strong electrostatic interaction, in which attractive ion‐ion correlation interactions appears, c) structure and stability of solutions of macroions with oppositely charged polyions added, and d) organization of magnetic particles with an off‐centered embedded magnetic dipole at zero and non‐zero magnetic field. Key references: a) Refs. [27, 28], b) [29, 30], c) [31, 32], and d) [33]. a) Reprinted with permission from J. Chem. Phys. 2014, 140, 044903. Copyright 2014, AIP Publishing LLC. b) Reprinted with permission from J. Chem. Phys. 2000, 113, 4359–4373. Copyright 2014, AIP Publishing LLC. c) Reprinted with permission from Macromolecules 2003, 36, 508–519. Copyright (2003) American Chemical Society.

Figure 11

Illustration of biocolloidal systems comprising a) the thermodynamic stability of virus‐capsid–genome complexation at different genome–capsid charge ratio and genome organization at different genome stiffness and b) study of the kinetics of the self‐ and co‐assembly of single‐stranded viruses. Key references: a) Refs. [34,35] and b) Refs. [36,37]. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Figure 12

Illustration of polymer systems investigated by the software MOLSIM. Key references: a) Refs. [38, 39], b) [40, 41], c) [42, 43], and d) [44, 45]. a) Reprinted with permission from J. Phys. Chem. B 2010, 114, 3741–3753. Copyright (2010) American Chemical Society. b) Reprinted with permission from Langmuir 2014, 30, 11117–11121. Copyright (2014) American Chemical Society. c) Reprinted with permission from Macromolecules 2002, 35, 5183–5193. Copyright (2002) American Chemical Society. Reprinted with permission from J. Phys. Chem. B 2003, 107, 8011–8021. Copyright (2003) American Chemical Society. d) Reprinted with permission from Langmuir 2004, 20, 10351–10360. Copyright (2004) American Chemical Society. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]

Figure 13

Illustration of crosslinked network systems comprising a) the swelling and structure of polyelectrolyte gels under a variety of alternating conditions and b) the impact of network imperfections and added macroions on the structure of polyelectrolyte gels. Polyelectrolyte gels consist of charged polymer networks, counterions, and solvent, and they are usually synthesized by chemically cross‐linking charged or titrating polymers. Key references: a) Refs. [46,47] and b) Refs. [48,49]. a) Reprinted with permission from J. Phys. Chem. B 2003, 107, 8030–8040. Copyright (2003) American Chemical Society. b) Reprinted with permission from Langmuir 2006, 22, 3836–3843. Copyright (2006) American Chemical Society. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]