Chemistry Reference
In-Depth Information
What Code?
As is apparent from the discussion of previous work, the most popular
simulation method in use right now to study ionic liquids is by far MD. Conse-
quently, very little phase behavior work has been done on ionic liquids but much
has been done on computing volumetric properties, liquid structure, and
dynamics. Part of the reason for this state of affairs is that there are a large num-
ber of MD codes available for free or at very low cost. Some of the more popular
ones that have been used for ionic liquid simulations include DL_POLY,
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NAMD,
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CHARMM,
137
LAMMPS,
122
GROMACS,
138
AMBER,
139
and
MDynaMix.
61
Each has a different input and output format, and loading the
correct force field parameters and other input commands can be tricky. Fortu-
nately, each program has reasonably good documentation and a large user base
that is good about answering questions. Each of the aforementioned programs
has strengths and weaknesses, so your choice of software will depend, to some
extent, on what properties you want to compute. We note in passing that com-
mercial vendors market software that can be used to run simulations of ionic
liquids. The advantage of using commercial software is that they come with
easy-to-use interfaces and more support; in our experience, however, these
codes tend to lag behind their open-source and academic rivals in terms of speed
and innovative features. Those companies all have sufficient promotional mate-
rials available so there is no need to discuss their products here, and we focus
only on noncommercial codes. For full disclosure, our group uses our own soft-
ware developed in-house over many years. For large-scale MD calculations, we
also use NAMD and LAMMPS.
NAMD is a very fast parallel MD code that scales to hundreds of pro-
cessors on the right architecture machine. On commodity clusters it scales
nicely to 32-128 processors. It is the recipient of the 2002 Gordon Bell award
and is well supported and documented by the Theoretical and Computational
Biophysics group at the University of Illinois. It may be downloaded from that
group's website (http://www.ks.uiuc.edu/Research/namd/). NAMD has as its
focus biophysics, so is not necessarily designed with ionic liquids in mind. It
mainly uses the protein data bank molecular structure format for input and
output of coordinates, which can become a bit unwieldy for ionic liquids. It
is helpful to construct molecules with standard molecular drawing software
and generate the requisite pdb files this way. NAMD is free and the source
code (written in C
) is distributed with the binaries, though we find modi-
fication of the source code to be a daunting task. It is compatible with the
popular molecular rendering package VMD
140
developed by the same group
at Illinois. Our group has used NAMD for several years whenever we needed
to run long MD simulations, and we find it to be efficient and relatively easy
to use.
LAMMPS is also a well-parallelized and fast MD code. It was designed
more for materials modeling and so in many ways is better suited than NAMD
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