We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder-Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment.
We have developed an automated parameter optimization software framework (ParOpt) that implements the Nelder-Mead simplex algorithm and applied it to a coarse-grained polarizable water model. The model employs a tabulated, modified Morse potential with decoupled short- and long-range interactions incorporating four water molecules per interaction site. Polarizability is introduced by the addition of a harmonic angle term defined among three charged points within each bead. The target function for parameter optimization was based on the experimental density, surface tension, electric field permittivity, and diffusion coefficient. The model was validated by comparison of statistical quantities with experimental observation. We found very good performance of the optimization procedure and good agreement of the model with experiment.
Water
plays a fundamental role in a wide range of fields of study,
including geology, atmospheric sciences, chemistry, biology, and physics.[1] Because of its relevance and ubiquity, water
is the most common solvent in experimental and computational studies
of biological systems.[2] The hydrophobic
effect, the segregation of molecules based on relative interactions
with water, governs membrane self-assembly, protein folding, and many
other biological processes.[3] Despite its
seemingly simple structure, the water molecule forms intricate and
dynamic networks of hydrogen bonds that give it unique bulk and interfacial
properties.[4,5] The wealth of anomalous characteristics
that water exhibits relative to most other liquids underscore its
uniqueness. In part because of its enigmatic character, it has been
the subject of many theoretical and modeling efforts in the past few
decades.[6] Reproducing these anomalous characteristics
poses a serious challenge for any effort to attain a detailed understanding
of water dynamics and structure.Quantum mechanical models of
water based on first principles (ab initio) precipitate
the evolution of the electronic structure
along with nuclear coordinates over time. The resolution of these
methods is at the level of molecular orbitals. These ab initio models produce radial distribution functions (RDFs) and rotational/vibrational
spectra that strongly agree with experimental data.[7,8] The
computational complexity of quantum models restricts systems to a
range too limited to determine most statistical bulk quantities. These
properties, such as the diffusion coefficient and thermodynamic variables,
are more accurately modeled by semiempirical approaches. Water models
with atomic-level detail are the most common for simulation of biomolecules
and their aggregates. To reproduce a wide range of complex water behavior,
several models that consist of four (Bernal–Fowler,[9] TIP4P,[10] and TIPS2[11]) and five (TIP5P[12]) interaction sites have been developed. In the interest of reducing
computational cost, most simulations use models (SPC,[13] SPC/E,[14] and TIP3P[15]) that are composed of three partially charged
atoms connected with rigid bonds and a Lennard-Jones (6-12) intermolecular
potential between oxygen atoms. Each model is reasonably accurate
within its domain of applicability, but none reproduce a large portion
of the anomalous properties of water. Various models[16] include flexible bonds that allow the water dipole moment
to change with the surrounding environment.Coarse-grained (CG)
models are able to achieve longer time scales
by averaging over rapid inter- and intramolecular motions, thus permitting
a larger time step. CG models are able to effectively represent a
larger number of molecules by reducing the number of interaction sites
considered. Because of the unusual properties of water, the development
of a CG model that reliably describes the bulk and medium-range properties
is a challenging project. The development of models of molecular assemblies
with lower complexity that reproduce important qualities of water[17,18] is ongoing. For an extensive review, see Coarse-Graining
of Condensed Phase and Biomolecular Systems.[19] Johnson et al.[20] have identified
limitations of CG models by demonstrating the lack of transferability
of a CG pair potential across different states. The work also shows
that the pair potential cannot simultaneously resolve all the properties
of the reference system for a given state. Despite these limitations,
there is extensive development of various CG models for water.[21−32] One common CG protocol is to group a number of water molecules into
a single bead with its center as the interaction site.[21−24,26,27,32] This class of CG models carries no charge.
Electrostatic interactions are implicitly incorporated into the effective
pairwise interaction potential which is either a Lennard-Jones (LJ)[21−24] or Morse-like function.[27] The free parameters
in pair potentials are trained against thermodynamic properties such
as density, surface tension, and solvation free energy. Molinero and
Moore[32] built a coarse-grained water model
around the tetrahedral properties shared by water, silicon, and carbon
by adapting the Stillinger–Webber potential originally developed
for silicon. The model maps one water molecule onto one interacting
bead and describes important properties of water across a wide range
of temperatures. Using a clustering algorithm, Hadley and McCabe derive
the effective potential through fitting to structural data.[17] The models of Shelley et al.[21] and Chiu et al.[27] have large
isothermal compressibility. Using a LJ 12-4 potential, Shinoda et
al.[24] have designed a CGwater that has
density and surface tension comparable to those of water. Electrostatic
interactions can be introduced into CGwater models with multiple
charged sites per bead.[25,28−31] These models can describe the dielectric properties of water. Despite
the incorporation of electrostatic interactions, both the BMW and
polarizable MARTINI models predict density different from experimental
measurements.[28,29] The CG representation of Darré
et al.[30] associates approximately 11 water
molecules with four tetrahedrally interconnected beads (WT4). The
model explicitly accounts for long-range electrostatics. The parameter
set of the WT4 model is tuned to match the experimental density. On
the other hand, the isothermal compressibility and surface tension
are modeled less accurately.[30] The recent
GROMOS CG[31] is a 5-to-1 mapped water model
with two electrostatic interaction sites. It delivers good results
for density, surface tension, and dielectric constant as compared
to those of real water but yields a coefficient of thermal expansion
1 order of magnitude higher than the experimental value. Adaptive
multiscale models allow transfer between simulation domains with differing
granularity, from the quantum level up to CG.[33−35] Adaptive methods
face unique challenges because of the variability in the degrees of
freedom over the span of a simulation. In continuation of our previous
CG development based on the Morse potential,[27] we upgrade our previous CGwater model (termed CSJ) with polarizability
and a Morse-like potential with more flexibility in the landscape
of pairwise interaction parameters. We will refer to the new model
as modified Morse coarse-grain (MMCG).
Model
A CG mapping of four water molecules to one CGwater bead was used
for the current model. For interactions between water beads, we have
further refined our previous model,[27] which
used the standard Morse potential, to meet two goals: (1) to improve
compressibility without sacrificing other features of the potential
and (2) to build into the interaction potential a smoothing function
that permits fairly accurate simulations using a shorter cutoff. The
choice of pairwise potential gives flexibility in the functional form
without introducing any extra simulation costs. The coarse-grained
potential must model the average of several different interatomic
and intermolecular forces. Therefore, the functional form is solely
based on a phenomenological understanding of the system rather than
a first-principle derivation, such as the r–6 behavior of the dispersion force included in the Lennard-Jones potential.
A modified Morse potential (eq 1) was used to describe interactions
between water bead centers.wherewhere R and De are the potential well location and depth, respectively.
Compared to the Morse potential, the MMCG potential replaces α,
the scaling parameter in the exponent, with two separate distance-dependent
variables, α(r) and β(r). This form decouples the repulsive (eq 1a) and attractive (eq 1b)
parts of the potential. The shape of the repulsive term as r tends to 0 is determined by α0. The exponential
factor tends toward αL as r approaches R. Parameters βR and βc provide similar behavior for the attractive part of the potential.
Beyond the cutoff distance rc, the potential
is taken to be 0. At this writing, we have not conducted an exhaustive
search for the value for rc that optimally
combines accuracy and efficiency, but the conventional value of 1.6
nm gives good results with reasonable efficiency. Comparing systems
representing equal numbers of water molecules, the MMCG model achieves
a >1 order of magnitude improvement in performance over an atomistic
system. The polarizability of CGwater beads is modeled like that
of the polarizable MARTINI water model,[28] through the addition of a harmonic angle potential term, with spring
constant K0 and equilibrium angle θ0, among three charged points. This model of polarizability
allows for not only dipole but also higher moments of the electrostatic
energy. Figure 1 provides an illustration of
the MMCG model. The central point, which acts as the interaction site
for the modified Morse potential, carries negative charge Q, while the two outer points each carry charge −Q/2. A mass equal to that of four water molecules is distributed
evenly among the three points. The distance between the outer points
and the central point is a tunable parameter I. The
change in the angle (θ) between the points represents the polarizable
nature of the bead. The set of potential parameters {De,R,α0,αL,βR,βc,θ0,K0,Q,I} determines
the space on which optimization will be performed.
Figure 1
Illustration of the MMCG model. Four water molecules map onto one
CG bead. Each CG bead has three charge sites. The central site with
charge Q provides the interaction site for the modified
Morse potential. Outer charge sites (with charge −Q/2) are connected to the central site by a fixed bond of length I. The central angle is a determined by a harmonic potential
with equilibrium angle θ0.
Methods and Results
Parameter Optimization
Parameter
optimization is exploration of a parameter space to determine extreme
values of a target function. In the case of molecular dynamics force
field optimization, the set of potential parameters defines the space
and comparison of model predictions with either ab initio data or experimental measurements defines the target function to
be minimized. We have developed a new software package, Parameter
Optimizer (ParOpt), for general optimization problems (ParOpt is available
for download under the GNU public license at https://csmlabfs1.cas.usf.edu/Sites). The software provides various optimization algorithms, including
an orthogonal steepest descent and the Nelder–Mead simplex-based
method. See Figure 2 for a schematic representation
of ParOpt. Target functions defined for molecular dynamics force field
optimization present a challenging problem. Sources of difficulty
include high dimensionality, discontinuities, possible stochasticity
due to random numerical error and finite sample size effects, and
difficulty in defining a derivative. Thus, in the context of molecular
dynamics parameter optimization methods such as simplex-based, approaches
with the least demanding conditions on the target function are the
most suitable. Nelder–Mead, a commonly used simplex-based optimization
algorithm, iteratively evolves M + 1 points on the M-dimensional space using four basic moves.[36]
Figure 2
Schematic representation of the ParOpt optimization framework.
ParOpt provides an environment in which different optimization methods
can be accessed by defining the generation of the target function.
Illustration of the MMCG model. Four water molecules map onto one
CG bead. Each CG bead has three charge sites. The central site with
charge Q provides the interaction site for the modified
Morse potential. Outer charge sites (with charge −Q/2) are connected to the central site by a fixed bond of length I. The central angle is a determined by a harmonic potential
with equilibrium angle θ0.Schematic representation of the ParOpt optimization framework.
ParOpt provides an environment in which different optimization methods
can be accessed by defining the generation of the target function.
Reflect
Replace the highest point
with a point reflected
about the centroid of the remaining points.
Expand
If the reflected point is lower in value than
all points in the centroid, consider a point further from the centroid.
Contract
If the reflected point would remain the highest,
consider a point nearer to the simplex.
Shrink
Move all points nearer to the lowest point.The M + 1 individual
points
in the M-dimensional space are denoted by P, while subscripts h and l
denote the lowest and highest points, respectively. The centroid is
defined byValues used for optimization of water parameters
are those suggested by Nelder–Mead:[23] α = 1.0, γ = 2.0, β = 0.5, and δ = 0.5.
Figure 3 graphically illustrates the Nelder–Mead
simplex transformations.
Figure 3
Schematic illustration of Nelder–Mead
steps. Arrows denote
points that will be replaced and the new point to be considered: (a)
the reflection of the highest point about the centroid of the remaining
points, (b) the further expansion of the reflection move, (c) the
contraction along the line joining the centroid and the highest point,
and (d) the shrinking of the simplex by shifting all points nearer
to the lowest point.
Schematic illustration of Nelder–Mead
steps. Arrows denote
points that will be replaced and the new point to be considered: (a)
the reflection of the highest point about the centroid of the remaining
points, (b) the further expansion of the reflection move, (c) the
contraction along the line joining the centroid and the highest point,
and (d) the shrinking of the simplex by shifting all points nearer
to the lowest point.The Nelder–Mead algorithm replaces the highest point
in
the simplex with one with a lower target function value by applying
these moves. A Nelder–Mead step begins with calculation of
a reflect move. If the target function value for this new reflected
point is lower than all points in the simplex, an expansion move is
attempted. If this expanded point is lower than all points in the
simplex, it is accepted. If the reflected point is not higher than
the highest point in the new simplex, it is accepted and replaces
the highest point in the simplex. If the newly accepted reflected
point is still the highest point in the simplex, a contraction step
is attempted. If the contracted point is higher than the highest point
in the simplex, then a shrink move is applied, replacing all points
except the lowest. If the contracted point is lower than at least
one point, it is accepted into the simplex. This process is repeated
until the stopping criterion is met. The stopping criterion for the
Nelder–Mead method is a cutoff on the root-mean-square target
function value over the entire simplex. The number of occurrences
of each move in an optimization depends on the characteristics of
both the simplex and the target function and is therefore problem
specific. The parameter space for the MMCGwater model is a 10-dimensional
bounded space. Minimal and maximal values (see Table 1) for each parameter were chosen heuristically to restrict
target function evaluations to reasonable combinations of parameters.
The original description of the Nelder–Mead algorithm has no
set method for boundary conditions on the parameter space, though
suggestions are made for modification of functional forms or assignment
of large “penalty” numbers for points outside of the
boundary. We chose to replace points outside the boundary with the
nearest point within the allowable space.
Table 1
Optimal
Parameters for a Set of Final
Parameters from Nelder–Mead Optimization Compared with Results
from the Previous Model (CSJ)
parameter
CSJ value[27]
optimized value
(this work)
minimal value
maximal value
De (kJ mol–1)
3.4
3.742
2.0
5.0
R (nm)
0.629
0.560
0.55
0.61
α0
7
15.545
7.0
20.0
αL
7
13.323
7.0
20.0
βR
7
10.976
7.0
20.0
βc
7
3.198
1.0
7.0
θ0
–
131.406
105.0
145.0
K0 (kJ mol–1)
–
93.918
20.0
180.0
Q (e)
–
–1.126
–1.6
–1.06
I (nm)
–
0.141
0.1
0.25
For optimization of
the MMCGwater model, the target function was
defined by the weighted percent error in comparison of CG simulation
results with four experimental quantities: density, dielectric constant,
diffusion coefficient, and surface tension. To ensure that all comparison
data contribute to the target function and thus the evolution of the
simplex, percent errors are assigned scalar weights to yield similar
orders of magnitude among all quantities. With this goal in mind,
density was weighted 100 times higher than surface tension, while
permittivity and diffusion coefficient were weighted 10 times higher.
Experimental values used in training are listed in Table 2.
Table 2
Training Data Showing Results for
the Optimized Point Compared with Experimental Target Data
property
experiment
training result
ρ (g cm–3)
0.996[39]
0.993
D (×10–9 m s–2)
2.597[40]
2.61
ε
76.8[41]
76.24
γ (mN m–1)
71.2[42]
78.43
Density
Density was computed by
taking the ratio of
the mass of the system and the ensemble average volume.
Diffusion
Coefficient
The standard practice in comparing
diffusion coefficients between CG models and experiment is to assume
that diffusion for N-sized clusters scales as 1/N; i.e., D = D1/N, where D is the diffusion coefficient
for an N-sized cluster. This assumption neglects
any interatomic correlation. The GROMOS CG work[31] compares the CG bead diffusion coefficient with the diffusion
coefficient for the center of mass of clusters in the SPC water model.
In that work, static clusters in the atomistic representation were
produced by adding distance restraints between oxygen atoms, which
produces diffusion coefficient scaling close to the inverse behavior
usually assumed. In the work presented here, clusters are constructed
similarly, though unrestrained. To calculate diffusion coefficient
scaling, clusters were constructed from each molecule and its nearest N – 1 neighbors. The MSD for such clusters was calculated
using a window averaging method with eq 7. Though
the method presented here may not be generalizable to all types of
clusters, it provides an improvement over current assumptions for
homogeneous systems. Figure 4 shows the diffusion
coefficient scaling for SPC/E water. The plot for atomistic water
shows significant deviation from the scaling behavior of uncorrelated
clusters, especially at larger values of N. Therefore,
approximations leading to 1/N scaling are more appropriate
at smaller cluster sizes. At a bead size of four water molecules,
the difference is significant. On the basis of this analysis, we use
a scale factor (s) of 3.16 to compare the CG diffusion
coefficient with experiment, instead of the usual factor of 4.where x(t) is the position of the
central bead at time t and
the broken brackets denote an ensemble average.
Figure 4
MSD scaling for SPC/E
water. The line shows the usual practice
of taking the diffusion of an N cluster beginning N times slower than the single molecule. SPC/E was determined
by simulation of SPC/E at 303 K. Clusters were chosen by the N – 1 nearest neighbors for each water molecule,
and the center of mass diffusion was calculated.
MSD scaling for SPC/E
water. The line shows the usual practice
of taking the diffusion of an N cluster beginning N times slower than the single molecule. SPC/E was determined
by simulation of SPC/E at 303 K. Clusters were chosen by the N – 1 nearest neighbors for each water molecule,
and the center of mass diffusion was calculated.
Relative Permittivity
The relative permittivity (ε)
was calculated using a Clausius–Mossotti-like equation with
a reaction field with an infinite dielectric constant (conducting
boundary conditions).[37]where M is the total system
dipole, ε0 is the permittivity of free space, ⟨V⟩ is the ensemble average system volume, T is the target temperature for the thermostat, and ε0 is the permittivity of the vacuum.
Surface Tension
The surface tension was taken from
the GROMACS internal calculation:where the z-axis is normal
to the interface, P terms are the pressure tensor diagonal elements, Ns is the number of interfaces, and L is the size of the system along the z-axis.The optimization procedure involves many target
function evaluations. These evaluations, at a point in parameter space,
involve the execution of two MD simulations. This places practical
limits on the size and length of simulations used for optimization.
Therefore, systems used for determination of the diffusion coefficient,
density, and electric field permittivity contained 512 CG beads, corresponding
to 2048 water molecules. This system is denoted as S1.
Because of large fluctuations, the calculation of surface tension
requires a larger system: 4096 CG beads, implying 16384 water molecules
(system S2). System S2 was constructed, at every
evaluation of the target function, with a slab near the average density
computed from S1 in contact with a vacuum.[38] System S2 was simulated under the constant number,
volume, and temperature (NVT) ensemble. More details
on simulation methods are found in Appendix A.The first step in optimization is the construction of an
initial
simplex. In this work, optimization started with a simplex consisting
of random points within the domain of parameter space that satisfied
constraints. This simplex was optimized until convergence. To further
improve the accuracy of the final point, the optimization was restarted
with an initial simplex consisting of the converged point and random
points around it. This procedure was then iterated two more times,
with the final optimization resulting in the point presented in Table 1.Figure 5 shows the
mean and root-mean-square
(rms) target function value versus the Nelder–Mead step for
the final optimization iteration. Because of the roughness of the
hypersurface generated by the target function, the simplex may occasionally
include a vertex with an abnormally high value, as observed in the
mean and rms of the second shrink step of Figure 5. Figure 6 shows the evolution of parameter
values over the final run, while Figure 7 shows
the change in computed physical properties. The figures demonstrate
the convergence of both the data and parameter values. Further, Figure 6 demonstrates that although parameters did encounter
the boundaries over the course of the optimization, the final simplex
converged away from the boundary. Thus, the parameter value boundaries
chosen were not unreasonable.
Figure 5
Optimization results. The mean error, rms error,
and rms cutoff
as a function of Nelder–Mead step are shown. Reflection (□),
contraction (○), and shrink (■) steps are labeled at
the corresponding mean error point.
Figure 6
Optimization results. Parameter trajectory. Variation in parameters
as a function of Nelder–Mead step. Dashed lines indicate minimal
and maximal values.
Figure 7
Optimization results.
Training data [density (ρ), electric
field permittivity (ε), diffusion coefficient (D), and surface tension (γ)] (—) as a function of Nelder–Mead
step compared with target values (---).
Optimization results. The mean error, rms error,
and rms cutoff
as a function of Nelder–Mead step are shown. Reflection (□),
contraction (○), and shrink (■) steps are labeled at
the corresponding mean error point.Optimization results. Parameter trajectory. Variation in parameters
as a function of Nelder–Mead step. Dashed lines indicate minimal
and maximal values.Optimization results.
Training data [density (ρ), electric
field permittivity (ε), diffusion coefficient (D), and surface tension (γ)] (—) as a function of Nelder–Mead
step compared with target values (---).The final set of parameters was chosen as the point in the
final
converged simplex with the lowest target function value (see Table 1). The decoupling of repulsive and attractive parameters,
the added distance dependence of the exponential factors, and the
added electrostatic interaction have allowed for a decrease in the
equilibrium distance, while maintaining the experimental density.
The large differences between exponential parameters in the new and
original models hint that the extensions have added important flexibility.
The simulation results corresponding to the final set of parameters
are listed in Table 2.
Validation
When validating the results
of an optimization procedure, one cannot consider the training data
alone. The suitability of the force field will depend on matching
data that the model was not explicitly trained to reproduce. Therefore,
validation simulations were performed to verify the reliability of
the optimized parameters. Because validation is not performed iteratively,
it is not subject to the same size constraints as optimization. All
systems for validation consisted of 110592 CG beads, which corresponds
to 442368 water molecules. See Appendix A for
more details on simulation methods.The density, diffusion coefficient,
relative permittivity, and surface tension were determined from the
larger validation systems using the same methods that were used during
optimization [see section 3.1; in addition,
bulk thermodynamic quantities were also calculated (see Table 3)].
Table 3
Validation Data Comparing Experimental
Data, an Existing CG Model (polarizable MARTINI), an Atomistic Model
(SPC/E), and the Previous Model (CSJ) to This Work (MMCG)a
property
experiment
polarizable
MARTINI[28]
SPC/E
CSJ[27]
MMCG
(this work)
ρ (g cm–3)
0.996[39]
1.043
0.998[14]
0.998
0.993 ±
0.0005
D (×10–9 m s–2)
2.597[40]
2.5
2.5[14]
4.3
3.07 ± 0.03
ε
76.8[41]
75.6
70.7 (at 298 K)[49]
74.17 ± 0.06
γ (mN m–1)
71.2[42]
30.5
71.0
78.73 ± 0.2
α (×104 K–1)
3.21[50]
6.89 ± 1.3
κT (×10–6 bar–1) (NPT)
44.75[51]
34.07[44]
170.0
68.95 ±
10
κT (×10–6 bar–1) (NVT)
44.75[51]
41.41[44]
57.16 ± 0.5
Hvap (kJ mol–1)
44.0[52]
38.4
48.52
Quantities computed are density
ρ, diffusion coefficient D, dielectric permittivity
ε, surface tension γ, coefficient of thermal expansion
α, isothermal compressibility κT, and enthalpy
of vaporization Hvap. Values computed
both during optimization and for validation differ because of the
size differences between simulated systems.
Coefficient of Thermal Expansion
The coefficient of
thermal expansion, α, was calculated using the finite-difference
method.[43]Two constant number, pressure, and temperature
(NPT) ensemble simulations at temperatures of 303.15
K (T1) and 308.0 K (T2) were performed. The ensemble averages of the resulting
densities were used for ρ1 and ρ2, respectively.
Isothermal Compressibility
Isothermal
compressibility
κT was calculated using two methods:[44] (i) a finite difference method for NVT simulations at different densities (ρ)and (ii) volume fluctuations in an NPT ensemble simulationwhere P is the pressure
on system i and ΔV2 is the variance of the volume. For eq 11,
the following densities were used: ρ1 = 0.993 g cm–3, and ρ2 = 0.963 g cm–3.
Enthalpy of Vaporization
The enthalpy of vaporization
was calculated from the interaction energy between CG beads (VInter) and the intermolecular interactions that
occur within the bead VS of 128.5 kJ mol–1 determined from quantum mechanical calculations of
the water tetramer binding energy.[27,45]where the factor of 4 is due to the level
of CG.The average dipole moment of an individual bead was calculated
for the MMCGwater model. Because a CG bead represents four water
molecules, the total dipole moment for an atomistically detailed SPC/E
water molecule along with its three nearest neighbors was computed
for comparison. The MMCG model yields an average dipole moment of
4.1 ± 0.25 D, whereas the four-water cluster dipole moment from
the SPC/E water model was 5.3 ± 1.0 D; density function theory
(DFT) calculations for an isolated cluster produce no dipole moment.[46] The effective polarizability (α0) for a CG bead was calculated using eq 14.[47] The MMCG model yields a value of 63 au compared
with a value of 39.33 au given by DFT for an isolated four-water cluster.[48] The disparity in these values is most likely
a result of differences between clusters in the bulk and in isolation.Quantities computed are density
ρ, diffusion coefficient D, dielectric permittivity
ε, surface tension γ, coefficient of thermal expansion
α, isothermal compressibility κT, and enthalpy
of vaporization Hvap. Values computed
both during optimization and for validation differ because of the
size differences between simulated systems.
Conclusion
To automate
force field optimization, we have developed a general
optimization framework ParOpt. The software utilizes various methods
to locate minima of the defined target function on parameter space.
Parameters are systematically varied to determine the most accurate
set of parameters. We have applied this general framework to optimize
the parameters of a polarizable CGwater model with nonbonded interactions
given by a modified Morse potential via the Nelder–Mead algorithm.
The model has more flexibility in the functional form than most CG
models, allowing it to match a wide range of experimental properties
(see Table 3).Any model in a classical
molecular dynamics framework is a simplification
of a physical system and therefore involves a reduction in the degrees
of freedom in the description of the interactions. Any such modeling
attempt would be nonunique. Though the set of parameters that govern
the model are mathematically independent, their effects on observable
data and therefore the target function are not necessarily uncorrelated.
Therefore, because of this interdependence of the parameters, the
optimization is not necessarily underdetermined despite an apparent
abundance of free parameters to match the target data. The question
of uniqueness is nontrivial to answer and is in fact a matter of ongoing
research (e.g., in the context of economic models[53]). For complex systems in general, there is no straightforward,
computationally tractable, and general solution to this problem; rather,
heuristic approaches must be developed for the particular system being
studied. In light of these factors, it may be the case that our parameter
set presented in this paper is one of many equally good sets. The
point we have chosen was a suitable point that matched the training
data well. Additionally, it can be seen from the good agreement with
the validation data, which is independent of the training data, that
the resulting force field parameters are well-tuned.There are
fundamental limitations to the explanatory power of CGwater models. RDFs are notoriously difficult for to match. An artifact
common to most CG models is the long-range correlation between CGwater beads not seen in experiment or atomistic models. Figure 8 shows that the current model suffers from that
same limitation. Likely as a result of the high degree of interbead
correlation at long distances, the model has the propensity to spontaneously
solidify at room temperature, a weakness found in other CGwater models.[23] This phenomenon would not be expected in a heterogeneous
system, because long-range correlations would be broken by the presence
of other interactions. Additionally, spontaneous freezing can be avoided
by periodically assigning random velocities chosen from a Maxwell
distribution, a method similar to one suggested by Harvey et al. to
prevent the overpopulation of low-frequency modes of a molecular dynamics
system.[54] Because dynamic and structural
properties of water clusters vary with temperature, the internal states
of CG beads would, as well. Thus, CG models cannot necessarily be
assumed to transfer to different temperatures. We believe that the
interaction parameters for CG models would be more accurately treated
as being temperature-dependent. The set of potential parameters has
been tuned for one temperature and is not expected to accurately simulate
behavior far from the target temperature or in thermodynamic ensembles
without constant temperature control.
Figure 8
RDF. Comparison between g(r)
for the atomistic SPC/E water model (—) and the MMCG water
model (---). The CG model has greater long-range coordination than
the atomistic model.
RDF. Comparison between g(r)
for the atomistic SPC/E water model (—) and the MMCGwater
model (---). The CG model has greater long-range coordination than
the atomistic model.The predictions of the model agree well with experiment for
structural,
dynamic, and bulk properties. The diffusion constant shows that the
model has accurate dynamics. The dielectric constant indicates the
validity of the parameters that determine electrostatics and polarizability.
Density ensures the correct spatial scale of the CG beads. Accurate
surface tension indicates an accurate representation of the strength
of the interaction between beads. The thermodynamic quantities predicted
by the model are in good agreement with those of experiment, validating
the fitness of the parameters.
Authors: Bernd Ensing; Steven O Nielsen; Preston B Moore; Michael L Klein; Michele Parrinello Journal: J Chem Theory Comput Date: 2007-05 Impact factor: 6.006
Authors: Siewert J Marrink; H Jelger Risselada; Serge Yefimov; D Peter Tieleman; Alex H de Vries Journal: J Phys Chem B Date: 2007-06-15 Impact factor: 2.991