MolecularDynamicsandMonteCarloSimulations

UrsulaRthlisberger

Lecture1

Adaptedfrom:
AbInitioMolecularDynamics
BasicTheoryandAdvancedMethods
DominiqueMarxandJurgHutter
CambridgeUniversityPress(2009)
Chapter2(pp.1120)
2
Getting started: unifying molecular dynamics and
electronic structure
2.1 Deriving classical molecular dynamics
The starting point of all that follows is non-relativistic quantum mechanics
as formalized via the time-dependent Schrodinger equation
(2.1)
in its position representation in conjunction with the standard Hamiltonian
n2 2 n2 2
H =- L: - \JI - L: - \J .
I 2MI i 2me
2
n2
= - L
2
M \?J + He({ri}, {RI})
I I
(2.2)
for the electronic { ri} and nuclear {RI} degrees of freedom. Thus, only
the bare electron-electron, electron-nuclear, and nuclear-nuclear Coulomb
interactions are taken into account. Here, MI and ZI are mass and atomic
number of the Jth nucleus, the electron mass and charge are denoted by
me and - e, and co is the vacuum permittivity. In order to keep the current
derivation as transparent as possible, the more convenient atomic units (a.u.)
will be introduced only at a later stage.
The goal of this section is to derive molecular dynamics of classical point
particles [25, 468, 577, 1189], that is essentially classical mechanics, starting
11
12 Getting started: unifying MD and electronic structure
from Schrodinger's quantum-mechanical wave equation Eq. (2.1) for both
electrons and nuclei. As an intermediate step to molecular dynamics based
on force fields, two variants of ab initio molecular dynamics are derived in
passing. To achieve this, two complementary derivations will be presented,
both of which are not considered to constitute rigorous derivations in the
spirit of mathematical physics. In the first, more traditional route [355]
the starting point is to consider the electronic part of the Hamiltonian
for fixed nuclei , i.e. the clamped-nuclei part He of the full Hamiltonian,
Eq. (2.2). Next, it is supposed that the exact solution of the corresponding
time-independent (stationary) electronic Schrodinger equation,
(2.3)
is known for clamped nuclei at positions {RI }. Here, the spectrum of He is
assumed to be discrete and the eigenfunctions to be orthonormalized
J 'l'"k({ri}; {RI} )'liz( {ri}; {RI}) dr = 8kl
(2.4)
at all possible positions of the nuclei; J dr refers to integration over all
i = 1, ... variables r = {ri}. Knowing all these adiabatic eigenfunctions at
all possible nuclear configurations, the total wave function in Eq. (2.1) can
be expanded
00
<I>({ri},{RI};t) = I:wz({ri};{RI})xz({RI};t) (2.5)
l = O
in terms of the complete set of eigenfunctions {'liz} of He where the nuclear
wave functions {xz } can be viewed to be time-dependent expansion coef-
ficients. This is an ansatz of the total wave function, introduced by Born
in 1951 [179, 811] for the time-independent problem, in order to separate
systematically the light electrons from the heavy nuclei [180, 771, 811] by
invoking a hierarchical viewpoint.
1
Insertion of this ansatz Eq. (2.5) into the time-dependent coupled Schro-
dinger equation Eq. (2.1) followed by multiplication from the left by
1
"The terms of the molecular spectra comprise, as is known, contributions of varying orders of
magnitude; the largest contribut ion originates from t he electron movement around the nuclei ,
there then follows a contribution stemming from the nuclear vibrations , and, ultimately, the
contribution arising from the nuclear rotation. The justificat ion of the existence of such a
hierarchy emanates from the magnitude of the mass of the nuclei, compared to that of the
electrons." Translated by the a ut hors from "Die Terme der Molekelspektren setzen sich bekan-
ntlich aus Anteilen verschiedener Gri:iBenordnung zusammen; der gri:iBte Beitrag riihrt von der
Elektronenbewegung urn die Kerne her, dann folgt ein Beitrag der Kernschwingungen, endlich
die von den Kernrotationen erzeugten Anteile. Der Grund fiir die Mi:iglichkeit einer solchen
Ordnung liegt offensichtlich in der GroBe der Masse der Kerne, verglichen mit der der Elektro-
nen. " Cited from the Introduction of the seminal paper [180] by Born and Oppenheimer from
1927.
2.1 Deriving classical molecular dynamics 13
wk({ri} ; {RI}) and integration over all electronic coordinates r leads to
a set of coupled differential equations
(2.6)
where
c., = j Wk [- ~
2
:
1
vi] w, dr
+ ~
1
2( {j wz [- in\7 1] Wz dr} [-in\7
1
] (2.7)
is the exact nonadiabatic coupling operator. The first term is a matrix
element of the kinetic energy operator of the nuclei, whereas the second
term depends on their momenta.
The diagonal contribution Ckk depends only on a single adiabatic wave
function W k and as such represents a correction to the adiabatic eigenvalue
Ek of the electronic Schrodinger equation Eq. (2.3) in this kth state. As
a result, the "adiabatic approximation" to the fully nonadiabatic problem
Eq. (2.6) is obtained by considering only these diagonal terms,
C
""" n2 j * 2
kk = - L......t
2
M
1
W k V' 1 \[! k dr ,
I
(2.8)
the second term of Eq. (2.7) being zero when the electronic wave function
is real, which leads to complete decoupling
(2.9)
of the fully coupled original set of differential equations Eq. (2.6). This,
in turn, implies that the motion of the nuclei proceeds without changing
the quantum state, k, of the electronic subsystem during time evolution.
Correspondingly, the coupled wave function in Eq. (2.1) can be decoupled
simply
(2.10)
into a direct product of an electronic and a nuclear wave function. Note
t hat this amounts to taking into account only a single term in the general
expansion Eq. (2.5).
14 Getting started: unifying MD and electronic structure
The ultimate simplification consists in neglecting also the diagonal cou-
pling terms
(2.11)
which defines the famous "Born-Oppenheimer approximation". Thus, both
the adiabatic approximation and the Born- Oppenheimer approximation (in-
troduced in Ref. [180] using a cumbersome perturbation expansion in powers
of the mass ratio (m
8
/MI)
1
1
4
, see also 14 and Appendix VII in Ref. [179])
are readily derived as special cases based on the particular functional ansatz
Eq. (2.5) of the total wave function. In the above simplified presentation
subtleties due to Berry's geometric phase [1329] have been ignored, but the
interested reader is referred to excellent reviews [168, 986, 1642] that cover
this general phenomenon with a focus on molecular systems.
The next step in the derivation of molecular dynamics is the task of ap-
proximating the nuclei as classical point particles. How can this be achieved
in the framework where a full quantum-mechanical wave equation, Xk, de-
scribes the motion of all nuclei in a selected electronic state \If k? In order
to proceed, it is first noted that for a great number of physical situations
the Born- Oppenheimer approximation can safely be applied, but see Sec-
tion 5.3 for a discussion of cases where this is not the case. Based on this
assumption, the following derivation will be built on Eq. (2.11) being the
Born- Oppenheimer approximation to the fully coupled solution, Eq. (2.6).
Secondly, a well-known route to extract semiclassical mechanics from quan-
tum mechanics in general starts with rewriting the corresponding wave func-
tion
(2.12)
in terms of an amplitude factor Ak and a phase Sk which are both considered
to be real and Ak > 0 in this polar representation, see for instance Refs. [345,
996, 1268]. After transforming the nuclear wave function in Eq. (2.11) for
a chosen electronic state k accordingly and after separating the real and
imaginary parts, the equations for the nuclei
ask "_1_ (\7
8
)2 E = n2" _1_ 'VJAk
at + 0 2M I k + k 0 2M A
I I I I k
(2.13)
(2.14)
2.1 Deriving classical molecular dynamics 15
using Rexk and Imxk. It is noted in passing that this quantum fluid dynamic
(or hydrodynamic, Bohmian) representation [169, 1636], Eqs. (2.13)-(2.14) ,
can actually be used to solve the time-dependent Schrodinger equation [340,
878].
The relation for the amplitude, Eq. (2.14), may be rewritten after multi-
plying by 2Ak from the left as a continuity equation [345, 996, 1268]
"' 1 ( 2 )
+ L_., M 'VI Ak V'ISk = 0
ut I I
(2.15)
(2.16)
with the help of the identification of the nuclear probability density Pk =
1Xkl
2
= obtained directly from the definition Eq. (2.12) , and with the
associated current density defined as Jk,I = This continuity
equation Eq. (2.16) is independent of nand ensures locally the conservation
of the particle probability density 1Xkl
2
of the nuclei in the presence of a
fl ux.
More important for the present purpose is a detailed discussion of the
relation for the phase Sk , Eq. (2.13), of the nuclear wave function that is
associated with the kth electronic state. This equation contains one term
that depends explicitly on n, a contribution that vanishes
(2.17)
:: t he classical limit is taken as n---+ 0. Note that a systematic expansion in
erms of n would, instead, lead to a hierarchy of semiclassical methods [562,
196]. The resulting equation Eq. (2.17) is now isomorphic to the equation of
ot ion in the Hamilton- Jacobi formulation [528, 1282] of classical mechanics
(2.18)
t he classical Hamilton function
(2.19)
:- a !ri.Yen conserved energy dEkot / dt = 0 and hence
aSk tot
8t =- (T + Ek) = - Ek = const.
(2.20)
16 Getting started: unifying MD and electronic structure
defined in terms of (generalized) coordinates {RI} and t heir conjugate canon-
ical momenta {PI}. With the help of the connecting t ransformation
[
Jk I]
PI= VISk = MI p ~
(2.21)
the Newtonian equations of motion, PI = -VI Vk( {RI} ), corresponding to
the Hamilton- Jacobi form Eq. (2.17) can be read off
dPI
dt = -\liEk or
.. BO
MIRI(t ) =-\l I Vk ( {RI (t)})
(2.22)
separately for each decoupled electronic state k. Thus, the nuclei move ac-
cording to classical mechanics in an effective potential, VkBO, which is given
by the Born- Oppenheimer potential energy surface Ek obtained by solving
simultaneously the time-independent electronic Schrodinger equation for the
kth state, Eq. (2.3), at the given nuclear configuration {RI(t)}. In other
words, this time-local many-body interaction potential due to the quantum
electrons is a function of the set of all cla ical nuclear positions at time
t. Since the Born- Oppenheimer total energie in a specific adiabatic elec-
tronic state yield directly the forces used in thi Yariant of ab initio molec-
ular dynamics, this particular approach is often called "Born- Oppenheimer
molecular dynamics", to be discussed in more detail later in Section 2.3.
In order to present an alternative deriYation. which does maintain a
quantum-mechanical time evolution of the electrons and thus does not in-
voke solving the time-independent electronic chrodinger equation Eq. (2.3)
as before, t he elegant route taken in Ref . [1516. 1517] is followed; see also
Ref. [943]. To this end, the nuclear and electronic contributions to the total
wave funct ion 1> ( { r i}. {RI}: t) are eparated directly such that , ultimately,
the classical limit can be impo ed for the nuclei only. The simplest possible
form is a product an atz
1>({ri} , {RI}:t) ~ w({r i} : t) \ ({RI}:t) exp [ ~ 1: Ee(t') dt'] ' (2.23)
where the nuclear and electronic waYe functio
to unity at every instant of time. i.e. (\: t l \: t
respectively. In addition. a pha e factor
are separately normalized
= 1 and (w; t lw; t) = 1,
Ee = J w*( {ri}; t) x*( {RI}: t ) He W( {r , }: t \ ( {RI} ; t ) drdR (2.24)
was introduced at this stage for conYenience -uch t hat the final equations
20 Getting started: unifying MD and electronic structure
electronic states W z
00
w({ri},{RI};t) = I:>z(t)Wz({ri};{RI})
(2.33)
l=O
with complex time-dependent coefficients { cz ( t)}. In this case, the coeffi-
cients lcz(tW satisfying :Z::::
1
Icz(tW = 1 describe explicitly the time evolution
of the populations (occupations) of the different states l whereas the nec-
essary interferences between any two such states are included via the off-
diagonal term, ck_cl=# One possible choice for the basis functions {wk} is the
instantaneous adiabatic basis obtained from solving the time-independent
electronic Schrodinger equation
(2.34)
where {RI} are the instantaneous nuclear positions at time t that are de-
termined acc6rding to Eq. (2.30). The actual equations of motion in terms
of expansion coefficients { ck}, adiabatic energies { Ek}, and nonadiabatic
couplings are presented in Section 2.2.
Here, instead, a further simplification is invoked in order to reduce Ehren-
fest molecular dynamics to Born- Oppenheimer molecular dynamics. To
achieve this, the electronic wave function W is restricted to be the ground
state adiabatic wave function Wo of He at each instant of time according to
Eq. (2.34), which implies lco(tW = 1 and thus a single term in the expansion
Eq. (2.33). This should be a good approximation if the energy difference
between Wo and the first excited state W1 is large everywhere compared to
the thermal energy kBT, roughly speaking. In this limit the nuclei move
according to Eq. (2.30)
~ E = J W
0
7-ie Wo dr =: Eo( {RI}) (2.35)
on a single adiabatic potential energy surface. This is nothing else than the
ground state Born- Oppenheimer potential energy surface that is obtained
by solving the time-independent electronic Schrodinger equation Eq. (2.34)
for k = 0 at each nuclear configuration {RI} generated during molecular
dynamics. This leads to the identification VeE =: Eo = V
0
80
and thus to
Eq. (2.22) , i.e. in this limit the Ehrenfest potential is identical to the ground
state Born- Oppenheimer (or "clamped nuclei") potential.
As a consequence of this observation, it is conceivable to fully decouple the
task of generating the classical nuclear dynamics from the task of computing
the quantum potential energy surface. In a first step, the global potential
energy surface Eo, which depends on all nuclear degrees of freedom {RI },
2.1 Deriving classical molecular dynami cs 21
is computed for many different nuclear configurations by solving t he sta-
t ionary Schrodinger equation separately for all these situations. In a second
step, these data points are fitted to an analytical functional form to yield
a global potential energy surface [1280], from which the gradients can be
obtained analytically. In a third step, the Newtonian equations of motion
are solved on this surface for many different initial conditions, producing a
"swarm" of classical traj ectories {RI ( t)}. This is, in a nutshell, the basis of
classical trajectory calculations on global potential energy surfaces as used
very successfully to underst and scattering and chemical reaction dynamics
of small systems in vacuum [1284, 1514] .
As already explained in the general introduction, Chapter 1, such ap-
proaches suffer severely from the "dimensionality as the number
of active nuclear degrees of freedom increases. One traditional way out of
this dilemma, making possible calculations of large systems, is to approxi-
mate the global potential energy surface
N N
VeFF({RI}) = :Lvl (RI) + L V2( RI , RJ)
l = l l<J
N
+ L v3( RI , RJ, Rx) + (2.36)
l<J<K
in terms of a truncated expansion of many-body contribut ions [25, 550, 577,
1405], which is sometimes called a "force field". At this stage, t he elec-
t ronic degrees of freedom are replaced approximately by a set of interaction
potentials { vn} and are no longer included as explicit degrees of freedom
when the nuclei are propagated. Thus, t he mixed quantum/ classical prob-
lem is reduced to purely classical mechanics, once t he { vn } are determined.
'Standard" molecular dynamics
(2.37)
relies crucially on such a force fi eld idea as opposed to ab initio molecu-
lar dynamics, either according to Born- Oppenheimer or Ehrenfest fl avor ,
where the key feature is that the potential and thus the forces are obtained
from solving the electronic structure problem concurrently to generating t he
t rajectory {RI(t)}.
In force field- based molecular dynamics, typically only two-body v2 or
t hree-body v3 interactions are taken into account [25, 468, 577, 1189], al-
t hough very sophisticated models exist that include nonadditive many-body
22 Getting started: unifying MD and electronic structure
interactions. This amounts to a dramatic simplification and removes, in
particular, the dimensionality bottleneck since the global potential surface
is reconstructed from a manageable sum of additive few-body contributions.
The flipside of the medal is the introduction of the drastic approximation
embodied in Eq. (2.36) , which basically excludes the study of chemical re-
actions from the realm of computer simulation.
As a result of the derivation presented above, the essential assumptions
underlying standard force field-based molecular dynamics become very trans-
parent. The electrons follow adiabatically the classical nuclear motion and
can be integrated out so that the nuclei evolve on a single Born- Oppenheimer
potential energy surface (typically, but not necessarily, given by the elec-
tronic ground state), which is generally approximated in terms of few-body
interactions.
Actually, force field-based molecular dynamics for many-body systems is
only made possible by somehow decomposing the global potential energy.
In order to illustrate this point, consider the simulation of N = 500 argon
atoms in the liquid phase [395] where the interactions can be described faith-
fully by additive two-body terms, i.e. L:::f<Jv2(IRI - RJI).
Thus, the determination of the pair potential v2 from ab initio electronic
structure calculations consists in computing and fitting a one-dimensional
function only. The corresponding task of determining a global potential en-
ergy surface, however, to doing that in about 10
1500
dimensions,
which is simply impossible. In the case of neat argon this is obviously not
necessary, but this assessment changes drastically if the 500 atoms are not
all identical and, for instance, are those that form a small enzyme catalyzing
a particular biochemical reaction.
2.2 Ehrenfest molecular dynamics
A systematic and general way out of the dimensionality bottleneck, other
than to approximate the global potential energy surface Eq. (2.36) or reduce
the number of active degrees of freedom, is to take seriously the classical
nuclei approximation to the TDSCF equations, Eqs. (2.30) and (2.32). This
implies computing the Ehrenfest force by actually solving numerically
MiRI(t) = -'\h j w*He'll dr
=-'VI (He) (2.38)