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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) from the group of Theodorou [11,12], were written in
codes, including LAMMPS,[1] NAMD,[2] Gromacs [3] Fortran 77. To re-use some of this code, the decision was
and DL_POLY.[4] Although the uses of MD vary widely, made to write the new code in Fortran 90, which allows for
the basic task of an MD code is generally the same: to user-defined data types and other features of object-
integrate Newton’s equations of motion and to generate a oriented programming but is also backwards compatible
trajectory in time for the particles. This contrasts with with Fortran 77.[13]
Monte Carlo, where a wider variety of ensembles and One difficulty in writing a general purpose code is
Monte Carlo moves have led to greater specialisation in handling the wide variety of force fields and move types.
codes. Many research groups that perform atomistic The design philosophy behind Music was to use object-
Monte Carlo simulations have developed and maintained oriented programming to provide generic interfaces that
their own codes. The number of publicly available, general can handle different move types and force fields. For
purpose, atomistic Monte Carlo codes is fairly limited and example, all calculations involving the force field, such as
includes MCCCS Towhee,[5] Etomica,[6] BOSS [7] and energy and force calculations, are wrapped into a force
DL_MONTE.[8] Among the commercially available field module. The interface receives the positions of all
simulation packages, Monte Carlo capabilities are atoms in the system and returns the energies (and forces if
available within Materials Studio by Accelrys [9] and needed) on particles of interest. This generic interface can
within Materials Design,[10] but the user may not have be plugged into any move type as described in more detail
access to the source code. by Gupta et al. [13]. The core functionalities of the Music
In this study, we review our experiences in developing code are summarised in Table 1. The primary developers
and releasing a multipurpose simulation code called of the code were Amit Gupta, Shaji Chempath, Martin
Music. Music is an object-oriented code, written in Fortran Sanborn and Louis Clark.
90, which provides functionality for performing MD A well-known issue with in-house academic codes is
simulations and Monte Carlo in a number of different the difficulty in motivating the code developers to write
ensembles, minimisations and free energy calculations in accurate and helpful documentation. Lack of adequate
bulk and adsorbed phases using a variety of force fields. manuals, tutorials and examples can lead to inappropriate
The code originated in the Snurr group in the late 1990s use of the code or interpretation of the results. A poorly
when students wanted to start using object-oriented described, undocumented code may need to be redeve-
programming features such as encapsulation and inheri- loped from scratch when the original developers leave the
tance to create a maintainable and extendible simulation research group. In the case of Music, a substantial effort
package. The group wanted a flexible code, capable of was invested in the development of appropriate documen-
both MD and Monte Carlo that would allow for the tation, test cases and description of the algorithms behind
development of new Monte Carlo simulation methods. The 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 downloaded the code and customised it for their own
western.edu/software.php) and Tina Düren’s web page at purposes. The authors do not foresee any updates to the
the University of Edinburgh (http://www.eng.ed.ac.uk/ official version of the code in the near future. The
, tduren/research/music/Tutorial/). remainder of this paper reviews some of the research
By 2003, a debugged, stable version of Music and its reported in the literature using the Music code, high-
documentation was ready, and we decided to make this lighting the code’s capabilities, along with some
version of the code publicly available under the GNU perspective from the experiences of the developers.
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 2. Monte Carlo simulations using Music
the group’s website in a password-protected section. Any Although Music includes a number of simulation
user who requests the password and agrees to the GPL is functionalities and features, the chart on the left of
given full access to the source code. Documentation is also Figure 2 indicates that in a vast majority of studies Music
available on the website. Since 2003, approximately 350 was employed in grand canonical Monte Carlo (GCMC)
users have requested the password, and the paper simulations, predominantly in the context of adsorption in
describing the code has been cited over 100 times, with porous materials. This section is dedicated to review some
a growing number of citations each year, as shown in of these studies. Other features of Music, including MD
Figure 1. Between 2003 and 2007, minor bug fixes and and more advanced, but less explored, applications are
upgrades were made to the official version of the code. reviewed in Section 3.
Since then, no updates have been made to the official The original purpose of Music was to provide a
version of the code, but many collaborators have 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]
Figure 1. Number of studies published each year since 2003 investigated adsorption of hydrogen, CO2, CH4, oxygen
that use Music as the primary simulation tool. Source: Thomson and nitrogen in decadodecasil 3R zeolite. With the rapid
Reuters ISI Knowledge. 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 surface chemistry, that can be tailored for particular
materials with a view to identify the best structure for a applications. Quite naturally, this has been an explosive
particular application and to understand what governs the area of research, with thousands of materials already
adsorption behaviour of these materials on a molecular reported. What has also become evident is that the current
level. An interesting example of this approach in zeolites is pace of new materials discovery exceeds the capacity to
provided by Fischer and Bell [29], who explored 18 zeolite test them experimentally for adsorption applications.
topologies (in purely siliceous composition) for adsorption Given the very large number of possible structures,
of CO2 and nitrogen. As the authors note, not all structures molecular simulations and virtual screening of porous
they explored correspond to real zeolites, as a majority of materials are becoming essential tools in the discovery
the zeolite structures have not been synthesised in their arsenal for nanoporous materials. This explains a
purely siliceous form. However, the conclusions of this substantial increase in recent applications of Music to
computational work can be extrapolated to real systems of adsorption in MOFs, COFs and other similar materials.
the same topology. The first simulation studies of adsorption in MOFs using
Recently, several new families of crystalline porous Music were conducted by Düren et al. [30] and Sarkisov
materials have emerged, such as metal-organic frame- et al. [31]. In the first study, adsorption of CH4 in several
works (MOFs) – including zeolitic imidazolate frame- MOFs was investigated and compared with that of other
works – and covalent organic frameworks (COFs). These materials such as MCM-41, carbon nanotubes and zeolites.
materials generally consist of vertices (formed by a metal The idea was to understand how various structural
complex or some other entity) connected by organic characteristics of porous materials are related to their
linkers. The virtually inexhaustible library of organic ability to store CH4 at 35 bar and room temperature
compounds implies an infinite number of possible (Figure 3). These particular conditions for CH4 storage are
materials with properties, such as pore dimensions and 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 mesoporous molecular sieves, and more exotic adsorbates,
alternative to compressed natural gas. This study high- such as volatile organic compounds and explosives, have
lighted the usefulness of computational tools for structural also been investigated.[67 – 72]
characterisation of MOF properties, such as accessible As Music was written using object-oriented program-
surface area, pore size distribution and so on, with these ming principles and following a set of rules outlined in the
tools later put together in a single simulation package by original paper,[13] changes and addition to the source
Sarkisov and Harrison [32]. The work also showed how code are (relatively) straightforward and users can adapt
these tools can be applied to porous material optimisation. Music to suit their own needs. In our eyes, this is one of the
Using insights from molecular simulations, the authors most attractive features of the code, and the following
suggested new not yet synthesised MOFs with CH4 paragraphs give a few examples from our own work that
adsorption characteristics exceeding the original target took advantage of this feature.
values, defined by the US Department of Energy. While classical potentials, such as Lennard-Jones
Interestingly, although the proposed materials have never (LJ) þ Coulomb, work well in many cases, they are unable
been synthesised, they inspired synthetic chemists to to properly describe hydrogen adsorption at low
temperatures where quantum effects play an important
search for materials with specific structural elements, and
role. Prosenjak et al. [35] extended Music to include a
indeed several materials have been later discovered with
second-order Feynman – Hibbs correction [73] to account
excellent CH4 storage characteristics based on these ideas.
for these quantum effects. This only involved changes in
[33] In the second study, adsorption and diffusion of linear
the module PairModels and programming a new object
alkanes and benzene were investigated in several crystal-
that contains the description of the Feynman – Hibbs
line MOFs and disordered metal-organic materials [31]
correction itself. These changes did not affect other objects
(see Figure 4). One of the interesting outcomes of that dealing with Monte Carlo moves or intramolecular
study was an observation of an analogy in the adsorption potentials. Prosenjak et al. then used this code to obtain
and transport properties between MOFs and zeolites with insights into the location of peaks in thermal desorption
pores of comparable size. spectroscopy of hydrogen in porous solids. In the thermal
Recent applications of Music to adsorption in MOFs desorption spectroscopy, a porous solid is first cooled to
and other similar materials are driven by the need to 20 K under hydrogen atmosphere, and then the tempera-
optimise materials for CH4 (natural gas) storage,[34] ture is slowly raised and the resulting desorption rate is
hydrogen storage,[35 –41] CO2 separations [42 – 47] and recorded. The Monte Carlo simulations of the hydrogen
other energy-related applications.[48 – 51] desorption spectra showed that the location of the peaks is
Music has also been applied to study adsorption in a directly related to the strength of the hydrogen – frame-
variety of carbon materials, including model carbon slit work interactions at different adsorption sites, demonstrat-
pores, fullerenes, nanotubes, C168 and so on, as well as ing that molecular simulations are a useful tool in the
aluminosilicate and boron nitride nanotubes.[26,30,52 – interpretation of these spectra.
66] Other materials, such as calixarenes, polymers and 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
Figure 4. Adsorption isotherms at 300 K for alkanes in IRMOF-
1: n-pentane (diamonds, solid line); cyclohexane (squares, solid the open metal sites, which cannot be achieved using a
line); n-hexane (circles, solid line) and n-heptane (triangles, solid simple LJ þ Coulomb force field. While this approach
line).[31] yields very accurate results, it is computationally
Molecular Simulation 1227

expensive to calculate a new potential energy surface for between asperities with increasing temperature and from
each new porous solid studied. Analytical expressions to squeezing out of lubricant molecules due to high loads on
describe the fluid – solid interactions are more convenient solid asperities. The solvation pressure is the pressure that
to use and are potentially transferable to other systems. In the lubricant exerts on the solid surfaces. If a load greater
an extension to their work, Chen et al. [75] fitted semi- than the fluid pressure is applied to a gap filled with
empirical model potentials to ab initio data using a genetic lubricant, the lubricant is squeezed out and the gap shrinks
algorithm and implemented these more complex poten- until the load meets a solvation force high enough to
tials, such as the Carra – Konowalow potential, into Music. balance it. While the solvation pressure can be studied
This approach allowed the correct description of CH4 and using conventional GCMC simulations, it is tedious to use
CO2 adsorption on MOFs with open metal sites, and there GCMC to study the solvation pressure of different
is some evidence that the potential parameters derived are lubricants, fluid pressures and temperatures. Simulations
transferable to other MOFs. in the grand isostress ensemble, where instead of the
In a GCMC simulation, using the different move types volume the stress normal to the walls is kept constant,
(translation, rotation, insertion and deletion), the number allow the effect of the load on the lubricant film to be
of molecules in a porous solid fluctuates and the average studied directly. In this ensemble, the applied load drives
value is reported as the amount adsorbed. In the case of the height of the gap to the equilibrium value where the
complex molecules such as long alkane molecules, the solvation pressure balances the applied load. As these
system can become trapped in a local energy minimum. simulations can test specific combinations of temperature
One indication of this is an acceptance probability for and load in a single simulation, they provide a much
molecule insertions and deletions which is virtually zero. quicker way to study lubricant failure. Severson et al.
In this case, the phase space is not sampled correctly. To modified Music to perform simulations in the grand
simulate the adsorption of long alkanes in the zeolite LTA- isostress ensemble, and were able to map out the failure
5A, Punnathanam et al. [22] extended Music to implement region as a function of temperature and applied load as
parallel tempering techniques to avoid this problem. Here, shown in Figure 5. Such failure maps could be used to
several replicas of the system are simulated in parallel with evaluate appropriate operating conditions for a particular
occasional swaps of configurations between the different lubricant/surface pair.
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 3. MD simulations with Music
zeolites with small windows. The simulations showed The MD capabilities of the Music code have been used by
good agreement with experimental data and captured various authors to study diffusion,[77 – 80] adsorption,
complex selectivity behaviour such as selectivity inversion [23,81] statistical mechanics of liquids [82] and tribology.
and azeotrope formation. [83] Compared with the usage of the GCMC module, the
Beyond the field of porous materials, Music has been usage of the MD module has been smaller, presumably
adapted to simulate tribology and the failure of lubricant because of the abundance of other MD packages available.
films. Lubricants protect surfaces by preventing solid – The MD modules in Music have also been used for
solid contact. Severson et al. [76] studied lubricant failure sampling within a Monte Carlo framework using hybrid
due to desorption of lubricant molecules from the gap Monte Carlo (HMC).[81] In our opinion, the flexibility

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.
1228 S. Chempath et al.

and object-oriented design of Music were key factors in CF4 in the zeolite faujasite. The evaluation of the Onsager
making some of these specialised calculations (e.g. non- coefficients (Figure 6) using Music also provided an
equilibrium molecular dynamics (NEMD), HMC or important mechanism for verifying theoretical predictions
tribology calculations) possible with minimal additional of binary diffusion starting with single component data.
coding effort. 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
3.1 MD in nanoporous materials prediction of multicomponent diffusivities. Here, MD
The ability to predict diffusion rates in nanoporous simulations played the important role of connecting theory
materials is important for the design of adsorption and experiment. These simulations validated a theory by
equipment such as pressure swing adsorption columns which experimentally measured (or calculated) single
and membrane-based separations. Numerous experimental component diffusivities can be used for predicting the
methods exist for measuring diffusion coefficients in multicomponent diffusion behaviour.
nanoporous materials, including pulsed field gradient Babarao and Jiang [85] studied the diffusion of pure
nuclear magnetic resonance, quasi-elastic neutron scatter- and mixed CH4 and CO2 in MFI, IRMOF-1 and C168
ing, zero-length column and microscopy. However, materials using Music. They evaluated self- and transport
historically, different experimental methods provided diffusion of pure components and mixtures and also
different values for the diffusion coefficients. MD evaluated the permselectivity of CO2 and CH4 for
simulations have therefore played a key role in improving evaluating the separation efficiency of these materials as
our understanding of diffusion in microporous materials membranes. They found C168 to be the most selective
and have helped bridge the gap between experiment and material but found that the selectivity for separation
theoretical models. The ability of Music to represent the decreases with increasing loading.
nanoporous sorbents using a potential map, allowing for Albo et al. [80] used a modified version of the Music
fast evaluation of the host –guest interactions, makes it code to study surface diffusion in nanopores. An analytical
especially suitable for studying diffusion along with potential map representing the LJ contributions of the pore
adsorption in materials such as zeolites and MOFs. (host) atoms was created and used in their work. They
Early applications of Music using MD involved the studied diffusion of ethane in alumina nanopores of
calculation of self-diffusivities and transport diffusivities diameter 10 –150 nm. Note that this is an order of
of sorbate molecules in zeolites.[77,78] While self- magnitude larger than the , 0.1 nm pores of zeolites. They
diffusivities are relatively easy to calculate, longer found that at elevated temperatures (under the range of
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. Figure 6. Chempath et al. calculated the Onsager coefficients
Lij from NEMD simulations for CH4 (1) and CF4 (2) in the zeolite
Chempath et al. [79] added an NEMD module, which
faujasite at 300 K. The lines represent predictions according to a
is part of the publicly released version of Music. In this theory based on the Maxwell –Stefan formulation of diffusion.
method, an external potential field is added to the force The squares, up triangles, down triangles and circles represent
field, where the potential field mimics the chemical L11, L12, L21 and L22, respectively. The cross coefficients (L12 and
potential gradient in the physical system. This NEMD 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
technique was found to be very efficient in evaluating the molecules/supercage of faujasite.[79] Source: Reprinted with
cross terms in the diffusivity matrix with acceptable error permission from Chempath et al. [79]. Copyright (2004)
bars. They studied binary mixtures of small alkanes and American Chemical Society.
Molecular Simulation 1229

pore sizes and conditions studied) surface diffusion is not


overall
the dominant mass-transport mechanism, but Knudsen nHB=6
nHB=5 0.01
diffusion dominates. 0.01 nHB=4
nHB=3
nHB=2
nHB=1

overall P(ε)
nHB=0

P(ε|nHB)
1e–06
3.2 MD as a sampling technique: HMC
Adsorption of rigid molecules can be studied with the 1e–06
standard moves used in GCMC simulations: insertion,
1e–10
deletion, rotation and translation. The internal flexibility of
molecules such as linear and branched alkanes can be
sampled with configurational-bias algorithms. However,
1e–10
complex molecules with ring structures (molecules with –40 –30 –20 –10 0 10
naphthenic rings or aromatic rings) require complicated ε, kcal/mol
moves (which must be developed and coded) to sample
their intramolecular degrees of freedom. Use of HMC as a Figure 7. (Colour online) Chempath et al. used the MD
modules in Music to sample the configurations of water
sampling technique was initially proposed by Duane et al. molecules in bulk and at the surface.[82] The binding energy
[86]. Two types of HMC moves were introduced into the distributions of water molecules in the bulk based on their
Music code for sampling the intramolecular degrees of hydration environment are shown. For example, the nHB ¼ 2
freedom of complex molecules. These moves work as curve corresponds to the probability distribution of the binding
energy of all molecules that have formed two hydrogen bonds.
whole-system moves, where the usual set of single-
Coloured symbols and lines are the observed probabilities and
molecule GCMC moves is interrupted periodically with an Gaussian fits, respectively. The overall distribution P(1) (plotted
HMC move in which the whole system is subject to a short on right y-axis) is obtained by adding the P(1jnHB) curves.[82]
MD simulation. The MD move is accepted or rejected at Source: Reprinted with permission from Chempath and Pratt
the end based on an energy criterion. Clark et al. [23] and [82]. Copyright (2009) American Chemical Society.
Chempath et al. [81] studied the adsorption of complex
molecules such as 1,2-dimethyl cyclobutane and dimethyl 4. Perspective and final comments
diphenyl allene in microporous materials using HMC. 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
3.3 MD and Monte Carlo of liquids using Music
group. However, one of the hallmarks of science is that
Chempath et al. [82,87,88] used the Music code to study each step forward builds on previous efforts. Making the
the statistical mechanics of aqueous phase solvation of Music code available has enabled a larger number of
different species in bulk and at an interface and to aid in researchers to build on the efforts of the code developers,
the development of a quasi-chemical theory of liquids. The who have, in turn, received significant satisfaction in
flexibility and object-oriented nature of Music made it seeing the range of problems addressed with the code. In
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 Figure 8. (Colour online) Martini et al. studied thin film
lubrication by simulating n-decane (lubricant) molecules
film thicknesses and found that the viscosity of thin films is between two parallel walls using NEMD.[83] Source:
subject to both shear thinning and oscillation with film Reprinted with permission from Martini et al. [83] with kind
thickness. permission of Springer Science and Business Media.
1230 S. Chempath et al.

addition, releasing the code under the GPL has helped in Carlo simulations with documentation and support
the continuous improvement of the code, as small but very comparable with that available for MD simulations.
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 Acknowledgement
is provided with no support. The original developers have R.Q.S. thanks the Department of Energy for support (DE-FG02-
tried to answer user questions when they have time, but 08ER15967).
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 References
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wider adoption of the code. However, all users have the Chipot C, Skeel RD, Kalé L, Schulten K. Scalable molecular
source code and can see exactly how the calculations are dynamics with NAMD. J Comput Chem. 2005;26:1781–1802.
[3] Berendsen HJC, van der Spoel D, van Drunen R. GROMACS: a
made and can write their own extensions of the code. message-passing parallel molecular dynamics implementation.
Releasing a code to other users raises (more than usual) Comput Phys Commun. 1995;91:43–56.
the question of code validation. As a normal part of our [4] Smith W, Yong CW, Rodger PM. DL_POLY: application to
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simulations results in the literature from other groups, [Internet]. [updated 2011 Aug 09]. Available from: http://towhee.so
sometimes communicating with those groups to verify urceforge.net
[6] Kofke DA, Schultz AJ. Etomica [Internet]. Available from: http://
particular details. When a version of Music was made www.etomica.org
available under the GPL, we included a set of case studies [7] Jorgensen WL, Tirado-Rives J. Molecular modeling of organic and
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