Molecular Simulation

ISSN: 0892-7022 (Print) 1029-0435 (Online) Journal homepage: http://www.tandfonline.com/loi/gmos20

Experiences with the publicly available

multipurpose simulation code, Music

Shaji Chempath, Tina Düren, Lev Sarkisov & Randall Q. Snurr

To cite this article: Shaji Chempath, Tina Düren, Lev Sarkisov & Randall Q. Snurr (2013)
Experiences with the publicly available multipurpose simulation code, Music, Molecular Simulation,
39:14-15, 1223-1232, DOI: 10.1080/08927022.2013.819103

To link to this article: https://doi.org/10.1080/08927022.2013.819103

Published online: 03 Sep 2013.

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Molecular Simulation, 2013
Vol. 39, Nos. 14 – 15, 1223–1232, http://dx.doi.org/10.1080/08927022.2013.819103

Experiences with the publicly available multipurpose simulation code, Music

Shaji Chempatha, Tina Dürenb, Lev Sarkisovb and Randall Q. Snurrc*
a
ExxonMobil Upstream Research Company, Houston, TX 77252, USA; bInstitute for Materials and Processes, School of Engineering,
The University of Edinburgh, Edinburgh EH9 3JL, UK; cDepartment of Chemical & Biological Engineering, Northwestern University,
Evanston, IL 60208, USA
(Received 6 May 2013; final version received 18 June 2013)

It has been 10 years since the original publication that presented Music, a multipurpose simulation code, written in Fortran
90. Since then, the code has been downloaded over 350 times and used in over 100 publications. In this study, we summarise
the philosophy behind Music, its features and capabilities, and review some recent applications of the code to problems
ranging from adsorption in porous materials to tribology and free energy analysis. We also reflect upon our experiences with
having a computer simulation code available to the public and highlight some current needs in the development of flexible,
versatile and well-documented software for Monte Carlo simulations.
Keywords: Monte Carlo; zeolites; metal-organic frameworks

1. Introduction group’s existing codes, which were descended largely

There are several widely used molecular dynamics (MD)
codes, including LAMMPS,[1] NAMD,[2] Gromacs [3]
and DL_POLY.[4] Although the uses of MD vary widely,
the basic task of an MD code is generally the same: to
integrate Newton’s equations of motion and to generate a
trajectory in time for the particles. This contrasts with
Monte Carlo, where a wider variety of ensembles and
Monte Carlo moves have led to greater specialisation in
codes. Many research groups that perform atomistic
Monte Carlo simulations have developed and maintained
their own codes. The number of publicly available, general
purpose, atomistic Monte Carlo codes is fairly limited and
includes MCCCS Towhee,[5] Etomica,[6] BOSS [7] and
DL_MONTE.[8] Among the commercially available
simulation packages, Monte Carlo capabilities are
available within Materials Studio by Accelrys [9] and
within Materials Design,[10] but the user may not have
access to the source code.
In this study, we review our experiences in developing
and releasing a multipurpose simulation code called
Music. Music is an object-oriented code, written in Fortran
90, which provides functionality for performing MD
simulations and Monte Carlo in a number of different
ensembles, minimisations and free energy calculations in
bulk and adsorbed phases using a variety of force fields.
The code originated in the Snurr group in the late 1990s
when students wanted to start using object-oriented
programming features such as encapsulation and inheri-
tance to create a maintainable and extendible simulation
package. The group wanted a flexible code, capable of
both MD and Monte Carlo that would allow for the
development of new Monte Carlo simulation methods. The
from the group of Theodorou [11,12], were written in
Fortran 77. To re-use some of this code, the decision was
made to write the new code in Fortran 90, which allows for
user-defined data types and other features of object-
oriented programming but is also backwards compatible
with Fortran 77.[13]
One difficulty in writing a general purpose code is
handling the wide variety of force fields and move types.
The design philosophy behind Music was to use object-
oriented programming to provide generic interfaces that
can handle different move types and force fields. For
example, all calculations involving the force field, such as
energy and force calculations, are wrapped into a force
field module. The interface receives the positions of all
atoms in the system and returns the energies (and forces if
needed) on particles of interest. This generic interface can
be plugged into any move type as described in more detail
by Gupta et al. [13]. The core functionalities of the Music
code are summarised in Table 1. The primary developers
of the code were Amit Gupta, Shaji Chempath, Martin
Sanborn and Louis Clark.
A well-known issue with in-house academic codes is
the difficulty in motivating the code developers to write
accurate and helpful documentation. Lack of adequate
manuals, tutorials and examples can lead to inappropriate
use of the code or interpretation of the results. A poorly
described, undocumented code may need to be redeve-
loped from scratch when the original developers leave the
research group. In the case of Music, a substantial effort
was invested in the development of appropriate documen-
tation, test cases and description of the algorithms behind
the code. These can be found on the Snurr group’s website

*Corresponding author. Email: snurr@northwestern.edu

q 2013 Taylor & Francis
1224 S. Chempath et al.

Table 1. Core functionalities in the original 2003 version of Music.

Methods Ensembles Systems Adsorbate species Properties

Monte Carlo NVT Confined Simple fluids Adsorption isotherms
mVT Bulk Rigid molecules Average potential energy
Linear chain molecules Pair distribution functions
Molecular dynamics NVE Confined Molecules of any geometry Self-diffusion coefficients
NVT Bulk and complexity Pair distribution functions
Average kinetic and potential energies
Analysis of molecular conformations
Hybrid Monte Carlo NVT Confined Molecules of any geometry Adsorption isotherms
mVT Bulk and complexity Average potential energy
Pair distribution functions

at Northwestern University (http://zeolites.cqe.north
western.edu/software.php) and Tina Düren’s web page at
the University of Edinburgh (http://www.eng.ed.ac.uk/
, tduren/research/music/Tutorial/).
By 2003, a debugged, stable version of Music and its
documentation was ready, and we decided to make this
version of the code publicly available under the GNU
Public License (GPL). A paper introducing the object-
oriented design of the code and some of the major data
structures was published,[13] and the code was placed on
the group’s website in a password-protected section. Any
user who requests the password and agrees to the GPL is
given full access to the source code. Documentation is also
available on the website. Since 2003, approximately 350
users have requested the password, and the paper
describing the code has been cited over 100 times, with
a growing number of citations each year, as shown in
Figure 1. Between 2003 and 2007, minor bug fixes and
upgrades were made to the official version of the code.
Since then, no updates have been made to the official
version of the code, but many collaborators have
Figure 1. Number of studies published each year since 2003
that use Music as the primary simulation tool. Source: Thomson
Reuters ISI Knowledge.
downloaded the code and customised it for their own
purposes. The authors do not foresee any updates to the
official version of the code in the near future. The
remainder of this paper reviews some of the research
reported in the literature using the Music code, high-
lighting the code’s capabilities, along with some
perspective from the experiences of the developers.
2. Monte Carlo simulations using Music
Although Music includes a number of simulation
functionalities and features, the chart on the left of
Figure 2 indicates that in a vast majority of studies Music
was employed in grand canonical Monte Carlo (GCMC)
simulations, predominantly in the context of adsorption in
porous materials. This section is dedicated to review some
of these studies. Other features of Music, including MD
and more advanced, but less explored, applications are
reviewed in Section 3.
The original purpose of Music was to provide a
versatile tool to explore the properties of fluids confined in
crystalline porous materials. Not surprisingly, early
applications of Music focused predominantly on zeolites.
These studies encompass a broad variety of adsorbate
molecules, ranging from single components and mixtures
of alkanes and aromatics [14 – 22] to chiral species [23]
and water.[24,25]
In recent years, there has been particularly strong
interest in application of porous materials to carbon
dioxide (CO2) separations, hydrogen storage and natural
gas purification and storage. Several groups have used
Music to study the behaviour of zeolites in these
applications. For example, adsorption of CO2 and methane
(CH4) in the zeolite silicalite was assessed and compared
with that of other materials by Babarao et al. [26], and
similar systems in faujasite were also investigated by
Ghoufi et al. [27]. In another example, Huth et al. [28]
investigated adsorption of hydrogen, CO2, CH4, oxygen
and nitrogen in decadodecasil 3R zeolite. With the rapid
advances in material science, molecular simulation has
 Molecular Simulation 1225

Figure 2. (a) Distribution of Music usage between GCMC simulations and other methods; (b) distribution of Music usage over different
types of materials investigated in adsorption simulation studies; (c) distribution of Music usage over different types of adsorbates
investigated in adsorption simulation studies. Light gases include hydrogen, nitrogen, oxygen, CH4, carbon dioxide and inert gases. Data
were collected from all published papers citing the Music code.[13]

emerged as a tool to screen through large sets of porous
materials with a view to identify the best structure for a
particular application and to understand what governs the
adsorption behaviour of these materials on a molecular
level. An interesting example of this approach in zeolites is
provided by Fischer and Bell [29], who explored 18 zeolite
topologies (in purely siliceous composition) for adsorption
of CO2 and nitrogen. As the authors note, not all structures
they explored correspond to real zeolites, as a majority of
the zeolite structures have not been synthesised in their
purely siliceous form. However, the conclusions of this
computational work can be extrapolated to real systems of
the same topology.
Recently, several new families of crystalline porous
materials have emerged, such as metal-organic frame-
works (MOFs) – including zeolitic imidazolate frame-
works – and covalent organic frameworks (COFs). These
materials generally consist of vertices (formed by a metal
complex or some other entity) connected by organic
linkers. The virtually inexhaustible library of organic
compounds implies an infinite number of possible
materials with properties, such as pore dimensions and
surface chemistry, that can be tailored for particular
applications. Quite naturally, this has been an explosive
area of research, with thousands of materials already
reported. What has also become evident is that the current
pace of new materials discovery exceeds the capacity to
test them experimentally for adsorption applications.
Given the very large number of possible structures,
molecular simulations and virtual screening of porous
materials are becoming essential tools in the discovery
arsenal for nanoporous materials. This explains a
substantial increase in recent applications of Music to
adsorption in MOFs, COFs and other similar materials.
The first simulation studies of adsorption in MOFs using
Music were conducted by Düren et al. [30] and Sarkisov
et al. [31]. In the first study, adsorption of CH4 in several
MOFs was investigated and compared with that of other
materials such as MCM-41, carbon nanotubes and zeolites.
The idea was to understand how various structural
characteristics of porous materials are related to their
ability to store CH4 at 35 bar and room temperature
(Figure 3). These particular conditions for CH4 storage are
important for the development of car fuelling systems

Figure 3. Amount of CH4 adsorbed in various materials (volumetric basis on the left and gravimetric basis on the right) at 35 bar and
room temperature as a function of accessible surface area. Source: Reprinted with permission from Düren et al. [30]. Copyright (2004)
American Chemical Society.
1226 S. Chempath et al.
based on adsorbed natural gas as an energy efficient
alternative to compressed natural gas. This study high-
lighted the usefulness of computational tools for structural
characterisation of MOF properties, such as accessible
surface area, pore size distribution and so on, with these
tools later put together in a single simulation package by
Sarkisov and Harrison [32]. The work also showed how
these tools can be applied to porous material optimisation.
Using insights from molecular simulations, the authors
suggested new not yet synthesised MOFs with CH4
adsorption characteristics exceeding the original target
values, defined by the US Department of Energy.
Interestingly, although the proposed materials have never
been synthesised, they inspired synthetic chemists to
search for materials with specific structural elements, and
indeed several materials have been later discovered with
excellent CH4 storage characteristics based on these ideas.
[33] In the second study, adsorption and diffusion of linear
alkanes and benzene were investigated in several crystal-
line MOFs and disordered metal-organic materials [31]
(see Figure 4). One of the interesting outcomes of that
study was an observation of an analogy in the adsorption
and transport properties between MOFs and zeolites with
pores of comparable size.
Recent applications of Music to adsorption in MOFs
and other similar materials are driven by the need to
optimise materials for CH4 (natural gas) storage,[34]
hydrogen storage,[35 –41] CO2 separations [42 – 47] and
other energy-related applications.[48 – 51]
Music has also been applied to study adsorption in a
variety of carbon materials, including model carbon slit
pores, fullerenes, nanotubes, C168 and so on, as well as
aluminosilicate and boron nitride nanotubes.[26,30,52 –
66] Other materials, such as calixarenes, polymers and
Figure 4. Adsorption isotherms at 300 K for alkanes in IRMOF-
1: n-pentane (diamonds, solid line); cyclohexane (squares, solid
line); n-hexane (circles, solid line) and n-heptane (triangles, solid
line).[31]
mesoporous molecular sieves, and more exotic adsorbates,
such as volatile organic compounds and explosives, have
also been investigated.[67 – 72]
As Music was written using object-oriented program-
ming principles and following a set of rules outlined in the
original paper,[13] changes and addition to the source
code are (relatively) straightforward and users can adapt
Music to suit their own needs. In our eyes, this is one of the
most attractive features of the code, and the following
paragraphs give a few examples from our own work that
took advantage of this feature.
While classical potentials, such as Lennard-Jones
(LJ) þ Coulomb, work well in many cases, they are unable
to properly describe hydrogen adsorption at low
temperatures where quantum effects play an important
role. Prosenjak et al. [35] extended Music to include a
second-order Feynman – Hibbs correction [73] to account
for these quantum effects. This only involved changes in
the module PairModels and programming a new object
that contains the description of the Feynman – Hibbs
correction itself. These changes did not affect other objects
dealing with Monte Carlo moves or intramolecular
potentials. Prosenjak et al. then used this code to obtain
insights into the location of peaks in thermal desorption
spectroscopy of hydrogen in porous solids. In the thermal
desorption spectroscopy, a porous solid is first cooled to
20 K under hydrogen atmosphere, and then the tempera-
ture is slowly raised and the resulting desorption rate is
recorded. The Monte Carlo simulations of the hydrogen
desorption spectra showed that the location of the peaks is
directly related to the strength of the hydrogen – frame-
work interactions at different adsorption sites, demonstrat-
ing that molecular simulations are a useful tool in the
interpretation of these spectra.
One way to speed up simulations in porous materials is
to record the potential energy that a guest atom
experiences due to the framework atoms on a rectangular
grid prior to the simulation.[11] During a simulation, the
potential energy of the fluid atom is then calculated by
interpolation using this potential energy ‘map’, which in
general is less time consuming than on-the-fly calcu-
lations. Music has the capability to create these potential
maps, but it can also use other potential maps as long as
they have the correct format. Chen et al. [74] implemented
a potential energy map calculated by a hybrid density
functional theory/ab initio method to describe CH4
adsorption at 77 K in HKUST-1, an MOF with open
metal sites. Note that CH4 was treated as a single site for
the simulations. A comparison of available experimental
adsorption isotherms and in situ X-ray diffraction data
showed that this approach captured the uptake and sitting
of the molecules accurately, including the interaction with
the open metal sites, which cannot be achieved using a
simple LJ þ Coulomb force field. While this approach
yields very accurate results, it is computationally

expensive to calculate a new potential energy surface for
each new porous solid studied. Analytical expressions to
describe the fluid – solid interactions are more convenient
to use and are potentially transferable to other systems. In
an extension to their work, Chen et al. [75] fitted semi-
empirical model potentials to ab initio data using a genetic
algorithm and implemented these more complex poten-
tials, such as the Carra – Konowalow potential, into Music.
This approach allowed the correct description of CH4 and
CO2 adsorption on MOFs with open metal sites, and there
is some evidence that the potential parameters derived are
transferable to other MOFs.
In a GCMC simulation, using the different move types
(translation, rotation, insertion and deletion), the number
of molecules in a porous solid fluctuates and the average
value is reported as the amount adsorbed. In the case of
complex molecules such as long alkane molecules, the
system can become trapped in a local energy minimum.
One indication of this is an acceptance probability for
molecule insertions and deletions which is virtually zero.
In this case, the phase space is not sampled correctly. To
simulate the adsorption of long alkanes in the zeolite LTA-
5A, Punnathanam et al. [22] extended Music to implement
parallel tempering techniques to avoid this problem. Here,
several replicas of the system are simulated in parallel with
occasional swaps of configurations between the different
replicas. This work showed that parallel tempering can
overcome many of the difficulties associated with the
simulation of liquid-phase alkane adsorption in cage-like
zeolites with small windows. The simulations showed
good agreement with experimental data and captured
complex selectivity behaviour such as selectivity inversion
and azeotrope formation.
Beyond the field of porous materials, Music has been
adapted to simulate tribology and the failure of lubricant
films. Lubricants protect surfaces by preventing solid –
solid contact. Severson et al. [76] studied lubricant failure
due to desorption of lubricant molecules from the gap
Figure 5. Left: Schematic of grand isostress simulations of pentadecane at a fluid pressure of 200 kPa and under a load of 1 GPa.
Increasing temperature allows more lubricant to be ‘squeezed’ out.[76] Right: Lubrication gap for several temperature-load combinations
for pentadecane at 200 kPa. Gaps less than 4 Å have no lubricant molecules in them.[76] Source: Reprinted from Severson et al. [76] with
kind permission of Springer Science and Business Media.
Molecular Simulation 1227
between asperities with increasing temperature and from
squeezing out of lubricant molecules due to high loads on
solid asperities. The solvation pressure is the pressure that
the lubricant exerts on the solid surfaces. If a load greater
than the fluid pressure is applied to a gap filled with
lubricant, the lubricant is squeezed out and the gap shrinks
until the load meets a solvation force high enough to
balance it. While the solvation pressure can be studied
using conventional GCMC simulations, it is tedious to use
GCMC to study the solvation pressure of different
lubricants, fluid pressures and temperatures. Simulations
in the grand isostress ensemble, where instead of the
volume the stress normal to the walls is kept constant,
allow the effect of the load on the lubricant film to be
studied directly. In this ensemble, the applied load drives
the height of the gap to the equilibrium value where the
solvation pressure balances the applied load. As these
simulations can test specific combinations of temperature
and load in a single simulation, they provide a much
quicker way to study lubricant failure. Severson et al.
modified Music to perform simulations in the grand
isostress ensemble, and were able to map out the failure
region as a function of temperature and applied load as
shown in Figure 5. Such failure maps could be used to
evaluate appropriate operating conditions for a particular
lubricant/surface pair.
3. MD simulations with Music
The MD capabilities of the Music code have been used by
various authors to study diffusion,[77 – 80] adsorption,
[23,81] statistical mechanics of liquids [82] and tribology.
[83] Compared with the usage of the GCMC module, the
usage of the MD module has been smaller, presumably
because of the abundance of other MD packages available.
The MD modules in Music have also been used for
sampling within a Monte Carlo framework using hybrid
Monte Carlo (HMC).[81] In our opinion, the flexibility
1228 S. Chempath et al.
and object-oriented design of Music were key factors in
making some of these specialised calculations (e.g. non-
equilibrium molecular dynamics (NEMD), HMC or
tribology calculations) possible with minimal additional
coding effort.
3.1 MD in nanoporous materials
The ability to predict diffusion rates in nanoporous
materials is important for the design of adsorption
equipment such as pressure swing adsorption columns
and membrane-based separations. Numerous experimental
methods exist for measuring diffusion coefficients in
nanoporous materials, including pulsed field gradient
nuclear magnetic resonance, quasi-elastic neutron scatter-
ing, zero-length column and microscopy. However,
historically, different experimental methods provided
different values for the diffusion coefficients. MD
simulations have therefore played a key role in improving
our understanding of diffusion in microporous materials
and have helped bridge the gap between experiment and
theoretical models. The ability of Music to represent the
nanoporous sorbents using a potential map, allowing for
fast evaluation of the host –guest interactions, makes it
especially suitable for studying diffusion along with
adsorption in materials such as zeolites and MOFs.
Early applications of Music using MD involved the
calculation of self-diffusivities and transport diffusivities
of sorbate molecules in zeolites.[77,78] While self-
diffusivities are relatively easy to calculate, longer
simulations are required to obtain converged results for
the transport (or Fickian) diffusivities. Transport diffusiv-
ity calculations include the evaluation of cross-velocity
correlation functions between molecules in the system.
Sanborn and Snurr [77,78] used MD to calculate transport
diffusivities for binary mixtures of alkanes and CF4 in the
zeolite faujasite. The predicted transport diffusivities were
then used to predict co-, counter- and osmotic diffusion
through faujasite membranes. One important aspect of
multicomponent diffusion calculations is that the deriva-
tives of fugacity with respect to the concentrations are
required. The GCMC modules in Music were used for such
calculations. Sanborn and Snurr [77] found that the
evaluation of the cross terms in the diffusion coefficient
matrix was difficult when one of the species was at low
concentrations.
Chempath et al. [79] added an NEMD module, which
is part of the publicly released version of Music. In this
method, an external potential field is added to the force
field, where the potential field mimics the chemical
potential gradient in the physical system. This NEMD
technique was found to be very efficient in evaluating the
cross terms in the diffusivity matrix with acceptable error
bars. They studied binary mixtures of small alkanes and
CF4 in the zeolite faujasite. The evaluation of the Onsager
coefficients (Figure 6) using Music also provided an
important mechanism for verifying theoretical predictions
of binary diffusion starting with single component data.
Chempath et al. [79] were able to verify a theoretical
method developed by Krishna and Baur [84], where single
component diffusivity data are the only input required for
prediction of multicomponent diffusivities. Here, MD
simulations played the important role of connecting theory
and experiment. These simulations validated a theory by
which experimentally measured (or calculated) single
component diffusivities can be used for predicting the
multicomponent diffusion behaviour.
Babarao and Jiang [85] studied the diffusion of pure
and mixed CH4 and CO2 in MFI, IRMOF-1 and C168
materials using Music. They evaluated self- and transport
diffusion of pure components and mixtures and also
evaluated the permselectivity of CO2 and CH4 for
evaluating the separation efficiency of these materials as
membranes. They found C168 to be the most selective
material but found that the selectivity for separation
decreases with increasing loading.
Albo et al. [80] used a modified version of the Music
code to study surface diffusion in nanopores. An analytical
potential map representing the LJ contributions of the pore
(host) atoms was created and used in their work. They
studied diffusion of ethane in alumina nanopores of
diameter 10 –150 nm. Note that this is an order of
magnitude larger than the , 0.1 nm pores of zeolites. They
found that at elevated temperatures (under the range of
Figure 6. Chempath et al. calculated the Onsager coefficients
Lij from NEMD simulations for CH4 (1) and CF4 (2) in the zeolite
faujasite at 300 K. The lines represent predictions according to a
theory based on the Maxwell –Stefan formulation of diffusion.
The squares, up triangles, down triangles and circles represent
L11, L12, L21 and L22, respectively. The cross coefficients (L12 and
L21) are scaled by a factor of 10, so that they can be plotted on the
same y-axis. The calculations were made at a loading of four
molecules/supercage of faujasite.[79] Source: Reprinted with
permission from Chempath et al. [79]. Copyright (2004)
American Chemical Society.

pore sizes and conditions studied) surface diffusion is not
the dominant mass-transport mechanism, but Knudsen
diffusion dominates.
3.2 MD as a sampling technique: HMC
Adsorption of rigid molecules can be studied with the
standard moves used in GCMC simulations: insertion,
deletion, rotation and translation. The internal flexibility of
molecules such as linear and branched alkanes can be
sampled with configurational-bias algorithms. However,
complex molecules with ring structures (molecules with
naphthenic rings or aromatic rings) require complicated
moves (which must be developed and coded) to sample
their intramolecular degrees of freedom. Use of HMC as a
sampling technique was initially proposed by Duane et al.
[86]. Two types of HMC moves were introduced into the
Music code for sampling the intramolecular degrees of
freedom of complex molecules. These moves work as
whole-system moves, where the usual set of single-
molecule GCMC moves is interrupted periodically with an
HMC move in which the whole system is subject to a short
MD simulation. The MD move is accepted or rejected at
the end based on an energy criterion. Clark et al. [23] and
Chempath et al. [81] studied the adsorption of complex
molecules such as 1,2-dimethyl cyclobutane and dimethyl
diphenyl allene in microporous materials using HMC.
3.3 MD and Monte Carlo of liquids using Music
Chempath et al. [82,87,88] used the Music code to study
the statistical mechanics of aqueous phase solvation of
different species in bulk and at an interface and to aid in
the development of a quasi-chemical theory of liquids. The
flexibility and object-oriented nature of Music made it
easy to add specialised calculations to the public version,
making it possible to collect, on-the-fly statistics on
binding energy and hydrogen bonding of different species
with high accuracy as shown in Figure 7.
3.4 Music in tribology
Martini et al. [83] used a modified version of Music to
study thin film lubrication. They used the GCMC module
to insert n-decane (lubricant) molecules between two
parallel walls and then conducted an NEMD simulation to
study viscous effects. The walls were moved at constant
speed as shown in Figure 8, and the temperature of the wall
atoms was kept constant with a Nose– Hoover thermostat,
while allowing the fluid to undergo viscous heating. They
also studied the variation in viscosity with different thin
film thicknesses and found that the viscosity of thin films is
subject to both shear thinning and oscillation with film
thickness.
Molecular Simulation 1229
overall
nHB=6
nHB=5 0.01
0.01 nHB=4
nHB=3
nHB=2
nHB=1
overall P(ε)
nHB=0
P(ε|nHB)
1e–06
1e–06
1e–10
1e–10
–40 –30 –20 –10 0 10
ε, kcal/mol
Figure 7. (Colour online) Chempath et al. used the MD
modules in Music to sample the configurations of water
molecules in bulk and at the surface.[82] The binding energy
distributions of water molecules in the bulk based on their
hydration environment are shown. For example, the nHB ¼ 2
curve corresponds to the probability distribution of the binding
energy of all molecules that have formed two hydrogen bonds.
Coloured symbols and lines are the observed probabilities and
Gaussian fits, respectively. The overall distribution P(1) (plotted
on right y-axis) is obtained by adding the P(1jnHB) curves.[82]
Source: Reprinted with permission from Chempath and Pratt
[82]. Copyright (2009) American Chemical Society.
4. Perspective and final comments
The decision to release the Music code was made only
after careful consideration. A highly functional, validated
code provides a significant advantage to a research
group. However, one of the hallmarks of science is that
each step forward builds on previous efforts. Making the
Music code available has enabled a larger number of
researchers to build on the efforts of the code developers,
who have, in turn, received significant satisfaction in
seeing the range of problems addressed with the code. In
Figure 8. (Colour online) Martini et al. studied thin film
lubrication by simulating n-decane (lubricant) molecules
between two parallel walls using NEMD.[83] Source:
Reprinted with permission from Martini et al. [83] with kind
permission of Springer Science and Business Media.
1230 S. Chempath et al.
addition, releasing the code under the GPL has helped in
the continuous improvement of the code, as small but very
useful improvements to the code and documentation have
been made, primarily based on the comments received
from other users. It should be noted, however, that the code
is provided with no support. The original developers have
tried to answer user questions when they have time, but
this has become increasingly difficult as they have taken
on other responsibilities in their careers. The code
developers do not have the resources to answer all user
questions, to add further functionality or to verify useful
additions from other groups. This has perhaps limited
wider adoption of the code. However, all users have the
source code and can see exactly how the calculations are
made and can write their own extensions of the code.
Releasing a code to other users raises (more than usual)
the question of code validation. As a normal part of our
research, we had validated our codes by reproducing
simulations results in the literature from other groups,
sometimes communicating with those groups to verify
particular details. When a version of Music was made
available under the GPL, we included a set of case studies
that new users can run to make sure that they obtain the
same results. This same set of case studies can be used to
test new versions of the code that have been modified to
include new functionality. We have used these case studies
internally to make sure that any new functionality does not
introduce errors into other parts of the code. We strongly
urge other groups making changes to Music to adopt this
same practice.
The Monte Carlo community would benefit signifi-
cantly if systematic test cases and procedures were
available for comparing different codes. We are not aware
of systematic and diligent comparisons of commercial and
freely available Monte Carlo codes for some well-known
and well-established systems, unlike in the MD field where
several benchmark calculations and performance com-
parisons have been made and published.[89 –91] This is
clearly a serious problem and something that we as a
community need to address.
The Music code is quite general, but its main strength
is for simulations of adsorbed phases. Limitations include
the inability to handle branched alkanes with configuration
bias and the inability to run in parallel. Growing interest in
porous materials for energy and environmental appli-
cations, such as gas separation and storage, as well as the
development of exciting new materials, such as MOFs, has
led to growth in the number of users of the code in the past
decade. More generally, we can anticipate the growing
importance of molecular simulation in the era of material
informatics. Computational screening and optimisation of
materials are poised to play an increasing role in the
development of new materials across a range of
applications. Hence, there will be a continuing need to
develop versatile, efficient and robust codes for Monte
Carlo simulations with documentation and support
comparable with that available for MD simulations.
Acknowledgement
R.Q.S. thanks the Department of Energy for support (DE-FG02-
08ER15967).
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