Computation of Pressure Components due to Class II

Force Fields
JOHN E. CARPENTER
SGI, 655F Lone Oak Drive, Eagan, Minnesota 55121

Received 9 April 2001; Accepted 11 December 2001

Published online 18 March 200 ). DOI 10.1002/jcc.10070

Abstract: It has been shown that purely angle dependent terms in a force field do not contribute to the total pressure
in a molecular simulation. However, this is not the case for the individual components of the pressure tensor, and is also
untrue for crossterms in the force field including bond stretch. In this article, we show that virial contributions to the
pressure tensor are easily computed in terms of bond distance vectors and atom forces for the bond topologies present
in a Class II force field. Results from a simulation of a phospholipid biomembrane using the cff97 force field show that
angle and torsional crossterms make a significant contribution to the pressure tensor.

© 2002 Wiley Periodicals, Inc. J Comput Chem 23: 667– 672, 2002

Key words: Class II forcefield; computation of virial; constant pressure molecular dynamics

Introduction Substitution of eqs. (1)–(3) into eq. (4) leads to the familiar
expression for the instantaneous total pressure
Computation of the instantaneous pressure tensor for a given force
field is required to carry out shape-varying constant pressure
冘
N
molecular dynamics simulations.1 Using momentum flux through 1
P⫽ 共m i␯ 2i ⫹ r i 䡠 Fi 兲 (5)
a plane cutting through each atom,2 this tensor is given by 3V
i⫽1

1 Analogously, the instantaneous scalar virial, W, is

P ␣␤ ⫽ 共2K ␣␤ ⫹ W ␣␤兲 (1)
V

冘
N
with 1
W⫽ 共W xx ⫹ W yy ⫹ W zz兲 ⫽ r i 䡠 Fi (6)
3
i⫽1

冘
N
1
K ␣␤ ⫽ m i␯ i␣␯ i␤ (2) For nonperiodic simulations, the virial is easily computed after
2
i⫽1 all contributions to the atomic forces have been accumulated using
eq. (6). However, as Brown has pointed out, the virial is not as
and easily computed for periodic simulations because forces arise from
interactions with image particles.3 Those forces must be multiplied
by the position of the image particle rather than the real particle

冘
N
when computing the virial. For this reason, contributions to the
W ␣␤ ⫽ r i␣F i␤ (3) virial are usually calculated at the same time as the atomic forces.
i⫽1
In this article, we will discuss how virial contributions from any
force field, particularly a Class II force field (see Appendix A), can
where V is the volume; m i , ri , vi , and Fi are the mass, position, be simply computed in terms of bond displacements and atomic
velocity, and force of atom i, respectively; ␣ and ␤ range over x, forces. The intramolecular part of a Class II force field, as defined
y, z. The quantity W in eq. (3) is known as the virial. The by Hwang et al.,4 is an anharmonic force field characterized by
instantaneous total pressure is given by

Correspondence to: J. E. Carpenter, Research Computing Facility,

1 Mayo Foundation for Medical Education and Research, 200 First Street
P ⫽ 共P xx ⫹ P yy ⫹ P zz兲 (4)
3 S.W., Rochester, MN 55905; e-mail: jec@mayo.edu

© 2002 Wiley Periodicals, Inc.

668 Carpenter • Vol. 23, No. 6
Morse or quartic bond stretching, quartic angle bending, one-,
two-, and three-fold torsion and crossterms. A number of investi-
gators, starting with Tominaga and Yip,5 have shown that force
field terms depending only on angle bending, torsional motion
(proper and improper), and/or a Wilson out-of-plane bend do not
contribute to the total pressure via the scalar virial. However, such
terms do contribute to the individual elements of the virial tensor.
Furthermore, a Class II force field includes cross terms that couple
bond stretch to angle bending and torsions. Such terms contribute
to the scalar virial, and therefore, the total pressure. The next
section of this article will present simple virial formulae based on
translational invariance for a general forcefield including a Class II
forcefield. Then this article presents simulation data showing the
relative contribution of different force field terms to the pressure
components for a spatially isotropic system, water, and a spatially
anisotropic system, an aqueous phospholipid bilayer. Finally, we
will discuss and summarize the findings of this work.
Virial Expressions for General Force Fields
A term in a general force field contributes to the forces of the
atoms involved in that term only. Likewise, a given force field
term only contributes to those atoms in the summation for the
virial [eq. (3)]. This makes it convenient to organize the compu-
tation of the virial by the number of bodies (atoms) involved in a
given force field term.
Two-Body Force Field Terms
The forces from a two-body potential such as a bond stretch or
central force expressions like a Lennard–Jones potential only
contribute to the virial given in eq. (3) for the two atoms a, b
involved
two-body
W ␣␤ ⫽ ra␣Fa␤ ⫹ rb␣Fb␤ (7)
If the two-body potential only depends upon the relative dis-
tance between the two atoms, the total force is zero.
F a␤ ⫹ Fb␤ ⫽ 0 (8)
In general, all intramolecular force field terms depend only
upon relative distances between atoms, thus making these terms
invariant to translation of the overall system. This can be combined
with eq. (6) to yield the familiar expression:
two-body
W ␣␤ ⫽ R␣abFa␤ (9)
where
R ␣ab ⫽ ra␣ ⫺ rb␣ (10)
This expression is computationally simple, and has the advan-
tage that R ab is likely to have been computed and adjusted for
periodic boundary conditions as part of the atomic force calcula-
tion making the virial computation quite efficient. Note, this for-
• Journal of Computational Chemistry
mula applies to any two-body interaction like a Lennard–Jones
nonbonded term or Coulombic interaction in addition to bond
stretch potentials like a harmonic or Morse potential.
Three-Body Force Field Terms
Like two-body force field terms, the forces due to a three-body
force field term only contribute to the virial for the three atoms
involved:
three-body
W ␣␤ ⫽ ra␣Fa␤ ⫹ rb␣Fb␤ ⫹ rc␣Fc␤ (11)
Again, making use of translational invariance of the sum of the
forces for this term
F a␤ ⫹ Fb␤ ⫹ Fc␤ ⫽ 0 (12)
the three-body virial contribution can be rewritten as
three-body
W ␣␤ ⫽ R␣abFa ␤ ⫹ R␣cbFc␤ (13)
where Rab and Rcb are defined analogously to eq. (10). This result
is also not new and is not unique. One could substitute for any of
the atomic forces using the translational invariance condition and
end up with variations of eq. (13) involving different combinations
of the atoms involved. The particular choice to substitute for the
force contribution to atom b yields the virial in terms of bond
vectors that are likely to have already been computed and adjusted
for periodic boundary conditions as part of the force calculation.
The conclusion of previous work5 is that purely angle-dependent
three-body force field terms do not contribute to the scalar virial
based on the fact that the gradient of the bond angle is orthogonal
to the associated bonds. However, a Class II force field like cff97
(see Appendix A) or the Merck Molecular Force Field, MMFF,6
includes bond bond and bond angle crossterms as part of the
three-body potential. The virial contributions from these terms as
well as the bond angle bending potential can be simply calculated
using eq. (13) with little computational cost and will contribute to
the overall scalar virial. Furthermore, as recognized by all previous
authors, individual terms of the virial are used when doing aniso-
tropic NPT simulations and so their contribution to the pressure
tensor should not be casually disregarded.
Four-Body Force Field Terms
A general four-body force field term such as a torsional term contrib-
utes to the virial for the four atoms involved. Four atoms can be
connected in two ways: linear (atom a is connected to b, b is con-
nected to c, c is connected to d) or trigonal (atoms a, c, and d are all
connected to atom b). After substitution for the force on atom b with
the negative of the sum of forces on the other three atoms due
translational invariance, the expression for virial contribution for a
linearly connected term like a torsional term can be rewritten as
linear
W ␣␤ ⫽ R␣abFa␤ ⫹ R␣cb共Fc␤ ⫹ Fd␤兲 ⫹ R␣dcFd␤ (14)
and for a trigonal term like a out of plane bending term
 Computation of Pressure Components 669

Table 1. Contributions to the Diagonal Elements of the Pressure Tensor from a NVT Simulation of Water in
PBC (1728 Molecules, 1 ⫽ 37.558 Angstroms, T ⫽ 300 K) Using the cvff Force Field with PPPM Long-
Range Electrostatics.

具W典/V

Two-body Three-body Four-body n-Body

2具K典/V nonbond Bond angle dihedral oop PPPM 具P典

xx 3999.2 20868.5 ⫺24786.1 ⫺25.4 na na ⫺2.2 53.9

rms 78.4 597.1 915.5 294.2 na na 139.9 986.4
yy 4001.9 20812.4 ⫺24789.7 32.8 na na 2.0 59.3
rms 79.3 567.1 923.6 290.5 na na 138.6 998.6
zz 4002.0 20855.8 ⫺24777.3 ⫺7.4 na na 1.4 74.6
rms 78.4 579.5 907.4 302.9 na na 140.9 987.0
total 4001.0 20845.6 ⫺24784.4 0.0 na na 0.4 62.6
rms 45.8 348.6 684.8 0.0 na na 80.2 704.2

All values were averaged over 100 picoseconds and are in atmospheres.

trigonal
W ␣␤ ⫽ R␣abFa␤ ⫹ R␣cbFc␤ ⫹ R␣dbFd␤ (15)
These expressions are similar to the Wilson S coordinate ex-
pression obtained by Tominaga and Yip (eqs. A22 and A14 of their
article5) except that they substituted for the force on atom c rather
than atom b in the torsional contribution to the virial. Either
expression would yield the same virial contribution. As noted for
the three-body virial contribution, other authors including Tomi-
naga and Yip have shown that eqs. (14) or (15) do not contribute
to the scalar virial due to the orthogonality of the bond vectors to
the gradient of the torsional or out of plane bend angles. In a Class
II force field, there are crossterms involving bond stretch with
torsion. These terms will contribute to the instantaneous total
pressure via the virial.
In summary, all virial contributions from a force field can be
computed via relatively simple expressions involved atomic forces
and bond displacements. Only those force field terms that involve
bond stretch will contribute to the instantaneous total pressure, but
all terms contribute to the individual terms of the instantaneous
pressure tensor.
Computations of the Pressure Tensor for a
Water System and an Aqueous Phospholipid
Bilayer Using Class I and Class II Force Fields
Computational Details
Four simulations were carried out on two systems using two force
fields. The two systems are an isotropic water box and an aqueous
phospholipid bilayer. The two forcefields are cvff,7 a Class I force
field, and cff97,8 a Class II force field.
All simulations presented here were carried out with the mo-
lecular dynamics program LAMMPS9 using a 0.5 femtosecond
time step in 3D periodic boundary conditions. Constant tempera-
ture and pressure constraints are implemented via Nose–Hoover
type thermostats and barostats in this program.10 Direct evaluation
of the Coulomb potential was cut off at 10 Angstroms, and the
Lennard–Jones potential was cut off at 12 Angstroms. All cutoffs
are atomic based with no smoothing or shifting. The neighbor list
was chosen out to 14 Angstroms. The long-range electrostatic
contribution was calculated using the PPPM methodology with a
32 ⫻ 32 ⫻ 32 FFT grid.11
The isotropic water box consisted of 1728 water molecules
originally arranged in a 12 ⫻ 12 ⫻ 12 grid with random orienta-
tions. This initial configuration was then simulated for approxi-
mately 500 picoseconds using a NPT ensemble at 1 atmosphere
and 300 K with both force fields (yielding average densities of
0.971 g/mL and 0.993 g/mL for the cvff and cff97 forcefields,
respectively). Following that, a sample configuration from near the
end of each NPT simulation was chosen as a starting point for a
100-picosecond NVT simulation at 300 K.
The aqueous phospholipid biomembrane consisted of 36 dimis-
torylphosphotidylcholine (DMPC) molecules arranged in a bilayer
(18 on each side) along the xz plane of the simulation cell with
1436 water molecules distributed on either side of the bilayer.
There are a total of 8556 atoms in the simulation cell. A starting
configuration of the phospholipid bilayer was obtained from Bris-
tol–Myers Squibb12 and simulated for over 1000 picoseconds
using a NPT ensemble at 1 atmosphere and 320 K with both force
fields. The x and z dimensions of the simulation cell were coupled
so as to retain the same fluctuating value thus conserving the two
dimensional symmetry of the simulation cell.13 This reduces rel-
atively meaningless fluctuations in the simulations. A representa-
tive configuration from near the end of the NPT trajectories was
chosen as the starting point for a corresponding 200-picosecond
NVT simulation at 320 K.
Simulation Results
Values for the various contributions to the diagonal elements of the
pressure tensor were averaged every MD step for the entire NVT
simulation in all four cases. Tables 1– 4 present these values (in
atmospheres) for the four simulations.
670 Carpenter • Vol. 23, No. 6 • Journal of Computational Chemistry

Table 2. Contributions to the Diagonal Elements of the Pressure Tensor from a NVT Simulation of Water
(1728 Molecules, 1 ⫽ 37.373 Angstroms, T ⫽ 300 K) in PBC Using the cff97 Force Field with PPPM
Long-Range Electrostatics.

具W典/V

Two-body Three-body Four-body n-Body

2具K典/V nonbond Bond angle dihedral oop PPPM 具P典

xx 4060.7 14039.8 ⫺20522.4 2428.0 na na ⫺0.4 5.7

rms 82.3 450.3 891.0 296.3 na na 144.1 958.4
yy 4060.7 14070.0 ⫺20512.2 2397.8 na na 2.2 18.5
rms 82.6 463.8 886.3 305.1 na na 143.4 947.6
zz 4060.7 14053.9 ⫺20512.8 2411.1 na na 2.7 15.8
rms 81.9 450.3 872.1 298.5 na na 143.0 941.4
total 4060.7 14054.6 ⫺20515.8 2412.3 na na 1.5 13.3
rms 46.3 301.2 640.4 201.4 na na 84.5 670.6

All values were averaged over 100 picoseconds and are in atmospheres.

Water
Tables 1 and 2 give the averages for the diagonal elements of the
pressure tensor components for the two water simulations. They
both exhibit the same general trends with some significant differ-
ences. Both show moderately large positive contributions to the
pressure tensor due to the kinetic energy, very large contributions
from the two-body interactions, and small contributions from the
angle bending and long-range electrostatic interactions. The two-
body contributions almost cancel each other. Both the size and sign
of the two-body pressure contributions result from the strong
directed hydrogen bond interaction between the oxygen on one
water molecule with near by hydrogen atoms on other water
molecules. The large partial charges on oxygen and hydrogen in
these force fields pull the atoms in the first solvation shell into
repulsive contact leading to large positive virial contributions. This
strong hydrogen bond, in turn, pulls the average OH bond length
out from its equilibrium position, which leads to almost propor-
tional negative virial contributions from the bond stretch term.
Table 2 shows that the cff97 two-body virial contributions are
smaller than the corresponding cvff values. This is due to the fact
that cff97 uses an anharmonic bond stretch potential and a Len-
nard–Jones 9-6 potential rather than a 12-6 potential. Both poten-
tials are “softer” than the corresponding functions in cvff.
The most noticeable difference between the cvff and cff97 pres-
sure components is due to the three-body terms in the force field. The
cvff three-body pressure components for water are relatively small
and sum to zero, as expected. Becker et al.5 have written that in the
limit of long time the individual elements of the virial due to angle
bending should be zero for an isotropic system like water. This system
of 1728 water molecules is not quite isotropic, and averaging for 100
picoseconds is probably not enough to see each diagonal element of
the average virial due to angle bending go to zero. The cff97 pressure
components for angle bending, on the other hand, are moderately
large and positive, and do not sum to zero. This is due to the

Table 3. Contributions to the Diagonal Elements of the Pressure Tensor from a NVT Simulation of a Lipid
Bilayer in PBC (36 DMPC Molecules, 1436 Water Molecules, l x ⫽ l z ⫽ 32.855 Angstroms, l y ⫽ 80.527
Angstroms, T ⫽ 320 K) Using the cvff Force Field with PPPM Long-Range Electrostatics.

具W典/V

Two-body Three-body Four-body n-Body

2具K典/V nonbond Bond angle dihedral oop PPPM 具P典

xx 4293.1 14553.2 ⫺19742.4 861.8 10.0 3.0 ⫺3.8 ⫺25.2

rms 72.3 354.1 801.4 307.8 7.5 49.0 90.4 896.0
yy 4293.1 18196.3 ⫺21114.3 ⫺1341.2 ⫺18.5 ⫺14.8 ⫺28.0 ⫺27.5
rms 72.1 364.1 786.0 305.4 6.2 27.7 171.0 907.5
zz 4293.1 15191.3 ⫺20067.3 479.4 8.5 11.9 5.3 ⫺77.7
rms 71.9 360.1 801.0 314.8 7.2 45.0 92.5 899.0
total 4293.1 15980.3 ⫺20308.0 0.0 0.0 0.0 ⫺8.8 ⫺43.5
rms 38.0 230.2 592.3 0.0 0.0 0.0 103.2 621.7

All values were averaged over 200 picoseconds and are in atmospheres.
 Computation of Pressure Components 671

Table 4. Contributions to the Diagonal Elements of the Pressure Tensor from a NVT Simulation of a Lipid
Bilayer in PBC (36 DMPC Molecules, 1436 Water Molecules, l x ⫽ l z ⫽ 35.926 Angstroms, l y ⫽ 67.980
Angstroms, T ⫽ 320 K) Using the cff97 Force Field with PPPM Long-Range Electrostatics.

具W典/V

Two-body Three-body Four-body n-Body

2具K典/V nonbond Bond angle dihedral oop PPPM 具P典

xx 4253.3 11688.4 ⫺13894.8 1127.5 ⫺3182.9 31.3 ⫺7.5 15.4

rms 70.3 310.5 801.4 334.5 117.4 32.5 103.0 885.4
yy 4253.3 13654.6 ⫺14570.2 60.1 ⫺3298.3 ⫺67.5 ⫺62.4 ⫺30.3
rms 70.4 307.1 786.0 330.2 102.4 31.3 163.9 890.9
zz 4253.3 11491.8 ⫺14130.0 1388.5 ⫺3018.2 36.2 1.7 23.4
rms 69.9 306.4 801.0 323.8 111.7 32.9 111.0 881.9
total 4253.3 12278.3 ⫺14198.3 858.7 ⫺3166.5 0.0 ⫺22.7 2.8
rms 37.2 211.7 587.6 237.5 73.4 0.0 119.2 609.5

All values were averaged over 200 picoseconds and are in atmospheres.

bond– bond and bond–angle crossterms in the cff97 force field, and
illustrates the key point of this article.
Aqueous Phospholipid Bilayer
Tables 3 and 4 give the averages for the components of the diagonal
elements of the pressure tensor for the aqueous phospholipid bilayer
using the cvff and cff97 force fields. Examination of these tables show
very similar trends to the water systems, but include contributions for
additional four-body force field terms (torsion and out-of-plane bend-
ing) that were not present in the water simulations. In addition, the
water system is approximately isotropic in all three dimensions,
whereas the bilayer is approximately isotropic in the plane of the
bilayer only. So, the 具Pxx典 and the 具Pzz典 components are similar while
being quite different from the 具Pyy典 values. Like the water system, the
two-body virial components are the largest and almost cancel each
other probably for the same reasons. The overall three-body virial
contributions are relatively larger in the bilayer system compared to
the water system, and exhibit strong spatial anisotropy. Although
larger, the cvff three-body virial contributions still sum to zero while
the crossterms in the cff97 force field make positive contributions to
all three spatial components. The cvff four-body torsion and out-of-
plane bending contributions are quite small compared to the other
contributions, and both sum to zero as expected. The cff97 four-body
torsion contributions are surprisingly large and negative due to the
bond torsion crossterms in the four-body part of the cff97 force field.
The cff97 four-body out-of-plane bending contributions are similar to
the cvff contributions and sum to zero because this term only depends
upon the out-of-plane bending angle.
term includes bond stretch. Simulations of a pure water system
using the cff97 force field yield three-body virial contributions that
are the same order of magnitude as the overall two-body virial
contribution while the four-body virial contributions in a simula-
tion of a phospholipid bilayer are even larger than the overall
two-body virial contribution. This suggests that pressure-depen-
dent properties should be checked when developing Class II type
force fields. The observation that the two two-body contributions
to the virial almost cancel, suggests that nearest neighbor nonbond
forces need to be evaluated on the same time scale as bond stretch
in a multiple time step method. This observation sets the stage for
further work.
Acknowledgments
The author wishes to thank SGI for the use of its Central Com-
puting Facility in Eagan, MN, and Dr. Terry Stouch (Bristol-Myers
Squibb) for the coordinates of the phospholipid bilayer as well as
his many comments and encouragement. Finally, Dr. Eric Simon
(Fordham College, NYC) did most of the Class II force field
coding in LAMMPS.
Appendix A
The Class II force field, cff97, can be expressed in five general
terms:

U cff ⫽ Uab ⫹ Uabc ⫹ Uabcd

torsion
⫹ Uabcd
oop
⫹ Unonbond (A1)
Summary and Conclusions
In the description of the force field terms to follow, a, b, c, d
The virial contribution to the pressure tensor can be easily calcu- denote bonded atoms; A, B, C, D their respective atom types; r ab,
lated in terms of bond distance vectors and atomic forces as long ␪abc, ␾abcd and ␹abcd denote bond distances, bond angles, torsions,
as the force field is invariant to overall translation. Application of and out-of-plane bends; K, r 0 , ␪0, and ␹0 are parameters.
these formulae shows that three- and four-body terms in a Class II The intramolecular two-body potential (bond stretching), U ab,
force field make a nonzero contribution to the total pressure if the is given by
672 Carpenter • Vol. 23, No. 6 • Journal of Computational Chemistry

冘冘
all bonds 4 where
U ab ⫽ k
K 共rab ⫺ r 兲
R
AB
0 k
AB (A2)
R ab k⫽2 1
␹៮ abcd ⫽ 共␹abcd ⫹ ␹cbda ⫹ ␹dbac兲 (A6)
3
The intramolecular three-body potential (angle bending, bond–
bond and bond–angle crossterms), U abc, is given by and ␹abcd is the angle between the bond ab with the plane defined

冘 冋冘
by atoms cbd. It may seem inappropriate to include the angle angle
all angles 4
crossterm with the out-of-plane term, but the atom connectivity is
␪
U abc ⫽ k
KABC 共␪abc ⫺ ␪ABC
0
兲k ⫹ KABC
RR
共rab ⫺ rAB
0
兲共rcb ⫺ rCB
0
兲 the same in each case.
␪ abc k⫽2 Finally, the intermolecular part of the cff97 force field is given

册
by
R␪ R␪
⫹ 共␪abc ⫺ ␪ABC
0
兲共1 KABC 共rab ⫺ rAB
0
兲 ⫹ 2 KABC 共rcb ⫺ rCB
0
兲兲

冘 冘冋 冉 冉 冊 冉 冊冊 册
N N⫺1
␴AB 9
␴AB 6
qaqb
U nonbond ⫽ ␧AB 2 ⫺3 ⫹ (A7)
(A3) rab rab rab
a⫽1 b⬍a

The intramolecular four-body potential is divided into two

terms. One is associated with a linear type of connectivity (i.e., References
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冘 冋冘
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␾
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U abcd ⫽ k
KABCD 共1 ⫺ cos共k␾abcd ⫺ k ␾ABCD
0
兲兲 rendsen, H. J. C.; van Gunsteren, W. F. J Comput Chem 1995, 16, 527;
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冉冘 冊
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3
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⫹ 共rab ⫺ rAB
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兲 k
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⫹ 共rcb ⫺ rCB
0
兲 k
KCB,ABCD cos共k␾abcd兲 7. Dauber–Osguthorpe, P.; Roberts, V. A.; Osguthorpe, D. J.; Wolff, J.;
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冉冘 冊
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␾R
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⫹ 共rdc ⫺ rDC
0
兲 k
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k⫽1 Chem 1994, 98, 8785.

冉冘 冊
8. Maple, J. R.; Hwang, M.-J.; Stockfisch, T.; Dinur, U.; Waldeman, M.;
3
␾␪
Ewig, C.; Hagler, A. T. J Comput Chem 1994, 15, 162; Hwang, M.-J.;
⫹ 共␪abc ⫺ ␪ABC
0
兲 k
KABC,ABCD cos共k␾abcd兲 Stockfisch, T.; Hagler, A. T. J Am Chem Soc 1994, 116, 2515; Ewig,
k⫽1 C. S.; Hagler, A. T. Comput Phys Commun 1994, 84, 131; Maple,

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J. R.; Hwang, M.-J.; Stockfisch, T. P.; Hagler, A. T. Isr J Chem 1994,
3
␾␪
34, 195; Peng, Z.; Ewig, C. S.; Hwang, M.-J.; Waldman, M.; Hagler,
⫹ 共␪dcb ⫺ ␪DCB
0
兲 k
KDCB,ABCD cos共k␾abcd兲 A. T. J Phys Chem A 1997, 101, 7243; Maple, J. R.; Hwang, M.-J.;
k⫽1
Jalkanen, K. J.; Stockfisch, T. P.; Hagler, A. T. J Comp Chem 1998,
␪␪␾
KABCD ⫹ 共␪abc ⫺ ␪ABC
0
兲共␪dcb ⫺ ␪DCB
0
兲cos共␾abcd兲 19, 430; Hwang, M.-J.; Ni, X.; Waldman, M.; Ewig, C. S.; Hagler,

册
A. T. Biopolymers 1998, 45, 435.
9. Plimpton, S. J.; Pollock, E. L.; Stevens, M. J.; Simon, E. J.; Carpenter,
⫹ KABCD
13
共rab ⫺ rAB
0
兲共rdc ⫺ rDC
0
兲 (A4) J. E.; Lustig, S. R.; Belak, J.; Stouch, T. R. Large Atomic and
Molecular Massively Parallel Simulator (LAMMPS), 1996. The cur-
rent version is LAMMPS 99. Contact sjplimp@sandia.gov for more
The out-of-plane bending potential is given by: information.
10. Melchionna, S.; Ciccotti, G.; Holian, B. L. Mol Phys 1993, 78, 533.

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all oop 11. Hockney, R. W.; Eastwood, J. W. Computer Simulation Using Parti-
␹ ␪␪ cles, Adam Hilger, 1988; Pollock, E. L.; Gosli, J. Comput Phys
U oop ⫽ KABCD 共␹៮ abcd兲2 ⫹ KABCD 共␪abc ⫺ ␪ABC
0
兲共␪abd ⫺ ␪ABD
0
兲
Commun 1996, 95, 93.
␹ abcd ␪ abc ␪ abd
12. See, for example, Stouch, T. R. Molecular Simulations, 1993, 10, 335.
(A5) 13. Carpenter, J. E., manuscript in preparation.