An Introduction To Advanced Molecular Dynamics Techniques

An Introduction to Advanced
Molecular Dynamics
Techniques
Marco Masia
Dipartimento di Chimica - Universit di Sassari
http://physchem.uniss.it/marco.masia
marco.masia@uniss.it
Molecular Dynamics - Bibliography

General References:
D. Frenkel & B. Smit: Understanding Molecular Simulation: From Algorithms to Applications
M. P. Allen & D. J. Tildesley: Computer Simulation of Liquids
M. Ferrario, G. Ciccotti & K. Binder: Computer Simulations in Condensed Matter: From Materials to
Chemical Biology
M. E. Tuckerman & G. J. Martyna, J. Phys. Chem. B 104, 159 (2000)
non-Hamiltonian Systems:
M. E. Tuckerman, C. J. Mundy & G. J. Martyna, J. Chem. Phys. 115, 1678 (2001)
M. E. Tuckerman, Y. Liu, G. Ciccotti & G. J. Martyna, Europhys. Lett. 45, 149 (1999)
Extended Lagrangian:
H. C. Andersen, J. Chem. Phys. 72, 2384 (1980)
G. J. Martyna, M. L. Klein & M. Tuckerman, J. Chem. Phys. 97, 2635 (1992)
G. J. Martyna, D. J. Tobias & M. L. Klein, J. Chem. Phys. 101, 4177 (1994)
Molecular Dynamics - Bibliography

On-the-fly optimization of point dipoles:
M.-L. Saboungi, A. Rahman, J. W. Halley & M. Blander, J. Chem. Phys. 88, 5818 (1988)
M. Sprik & M. L. Klein, J. Chem. Phys. 89, 7556 (1988)
M. Sprik, J. Phys. Chem. 95, 2283 (1991)
M. Wilson & P. A. Madden, J. Phys.: Condens. Matter. 5, 2687 (1993)
Constraints:
J. P. Ryckaert, G. Ciccotti & H. C. J. Berendsen, J. Comp. Phys. 23, 327 (1977)
H. C. Andersen, J. Comp. Phys. 52, 24 (1983)
M. Sprik, Faraday Discuss. 110, 437 (1998)
M. Sprik & G. Ciccotti, J. Chem. Phys. 109, 7737 (1998)
N. Doltsinis & M. Sprik, Phys. Chem. Chem. Phys. 5, 2612 (2003)
I. Coluzza, M. Sprik & G. Ciccotti, Mol. Phys. 101, 2885 (2003)
N. Doltsinis, Computational Nanoscience: Do it Yourself!, pp. 375-387 (2006), free download available at
http://www.fz-juelich.de/nic-series/volume31.
Molecular Dynamics
In Molecular Dynamics the Lagrangian and the Hamiltonian have the following form:
Molecular Dynamics
L(rN , r N ) =
N
!
mi
i=1
r i r i
!
i<j
u(rij )
Molecular Dynamics
L(r , r ) =
N
N
!
mi
i=1
r i r i
!
i<j
u(rij )
L
pi =
= mi r i
r i
Molecular Dynamics
L(r , r ) =
N
N
!
mi
i=1
N
!
r i r i
!
i<j
u(rij )
L
pi =
= mi r i
r i
N
!
!
1
u(rij )
H(rN , pN ) =
r i pi L =
pi pi +
2mi
i<j
i=1
i=1
Molecular Dynamics
L(r , r ) =
N
N
!
mi
i=1
r i r i
u(rij )
i<j
L
pi =
= mi r i
r i
N
!
N
!
!
1
u(rij )
H(rN , pN ) =
r i pi L =
pi pi +
2mi
i<j
i=1
i=1
dri
H
pi
=
=
dt
pi
mi
dpi
H
=
=
dt
ri
N
!
j!=i
rij u" (rij )
Equations
of Motion
Molecular Dynamics
Some Questions:
Molecular Dynamics
Some Questions:
How shall we integrate the equations of motion?
Molecular Dynamics
Some Questions:
Which statistical mechanical ensemble do we sample?
Molecular Dynamics
Some Questions:
How could we sample other ensembles?
Molecular Dynamics
Some Questions:
How could we include many body effects (polarization)?
Molecular Dynamics
Some Questions:
How we deal with systems with different time scales?
Molecular Dynamics
Some Questions:
How could we include constraints in our system?
Molecular Dynamics
Some Questions:
HOW COULD WE COMPUTE THE DYNAMICS USING AN AB-INITIO

POTENTIAL?
Molecular Dynamics
Molecular Dynamics
The equations of motion are propagated in time through the classical propagator:
iLt
x(t) = e
x(0)
Molecular Dynamics
iLt
x(t) = e
x(0)
If the Liouville operator could be written as a sum of two operators, the classical
propagator could be rewritten making use of the Trotter theorem:
!
"
#
"
#
"
#$P
iL2 t
iL1 t
iL2 t
exp(iLt) = exp [(iL1 + iL2 )t] = lim exp
exp
exp
P
2P
P
2P
Molecular Dynamics
iLt
x(t) = e
x(0)
!
"
#
"
#
"
#$P
iL2 t
iL1 t
iL2 t
exp
exp
P
2P
P
2P
For finite P we define t = t/P and we approximate the classical propagator as:
Molecular Dynamics
iLt
x(t) = e
x(0)
!
"
#
"
#
"
#$P
iL2 t
iL1 t
iL2 t
exp
exp
P
2P
P
2P
exp(iLt) exp(iL2 t/2) exp(iL1 t) exp(iL2 t/2) + O(t3 )
Molecular Dynamics
iLt
x(t) = e
x(0)
!
"
#
"
#
"
#$P
iL2 t
iL1 t
iL2 t
exp
exp
P
2P
P
2P
exp(iLt) exp(iL2 t/2) exp(iL1 t) exp(iL2 t/2) + O(t3 )

exp(iLP t)
P
!
k=1
exp(iL2 t/2) exp(iL1 t) exp(iL2 t/2) + O(tt2 )
Molecular Dynamics
Given the Liouville operator:
# !
#
N "
N "
!
pi
H
=
+ Fi
iL = {. . . , H} =
pi ri
ri pi
mi ri
pi
i=1
i=1
Molecular Dynamics
# !
#
N "
N "
!
pi
H
=
+ Fi
iL = {. . . , H} =
pi ri
ri pi
mi ri
pi
i=1
i=1
Lets consider the following partition:
N
!
pi
iL1 =
m
r
i
i
i=1
N
!
Fi
iL2 =
p
i
i=1
Molecular Dynamics
# !
#
N "
N "
!
pi
H
=
+ Fi
iL = {. . . , H} =
pi ri
ri pi
mi ri
pi
i=1
i=1
N
!
pi
iL1 =
m
r
i
i
i=1
The operator
exp(iL1 t)
acts as a translation operator on

particles positions:
ri ri + t(pi /mi )
N
!
Fi
iL2 =
p
i
i=1
Molecular Dynamics
# !
#
N "
N "
!
pi
H
=
+ Fi
iL = {. . . , H} =
pi ri
ri pi
mi ri
pi
i=1
i=1
N
!
pi
iL1 =
m
r
i
i
i=1
The operator
exp(iL1 t)
acts as a translation operator on

particles positions:
ri ri + t(pi /mi )
N
!
Fi
iL2 =
p
i
i=1
Since forces depend only on the
particles positions, the operator
exp(iL2 t/2)
becomes a translational operator on

the momenta:
pi pi + (t/2)Fi (r)
Molecular Dynamics
The action of the operator exp(iLP t) on the full set of momenta and positions
can be evaluated analytically, yielding the following approximate evolution equations:
Molecular Dynamics
t2
ri (t) = ri (0) + vi (0)t +
Fi (0)
2mi
t2
vi (t) = vi (0) +
[Fi (0) + Fi (t)]
2mi
These equations constitute

the so-called velocity Verlet
integrator. According to the
approximate propagator
expression, we can look at
the integration procedure as
if it was a set of three
sequential updates:
Molecular Dynamics
t2
ri (t) = ri (0) + vi (0)t +
Fi (0)
2mi
t2
vi (t) = vi (0) +
[Fi (0) + Fi (t)]
2mi
These equations constitute

the so-called velocity Verlet
integrator. According to the
approximate propagator
expression, we can look at
the integration procedure as
if it was a set of three
sequential updates:
do i = 1,N
1) first velocity translation

2) position translation
vi vi + Fi t/2mi
ri ri + vi t
enddo
get new forces
do i = 1,N
3) second velocity translation
Fi
vi vi + Fi t/2mi
enddo
Molecular Dynamics
Some Remarks:
Molecular Dynamics
Some Remarks:
The procedure of translating each operator into an update step which
can be implemented in a computer code is called direct translation
technique;
Molecular Dynamics
Some Remarks:
technique;
Although such procedure may seem involved compared to the typical
approaches based on truncating Taylor expansions of the finite difference
equations, it proves to be immensely powerful in deriving the integration
schemes of complex non-Hamiltonian systems (see next slide), and to treat
systems with multiple time scale motion.
Molecular Dynamics
Some Remarks:
technique;
The map generated using the direct translation technique preserves the
invariant phase space measure; maps with this property are said to
symplectic. For Hamiltonian systems it means that the Jacobian is unit;
Molecular Dynamics
Some Remarks:
technique;
The map generated using the direct translation technique preserves the
invariant phase space measure; maps with this property are said to
symplectic. For Hamiltonian systems it means that the Jacobian is unit;
The symplectic property ensures that the integration error is bounded
and does not cause any growth in energy conservation.
Molecular Dynamics
In the case of non-Hamiltonian systems it has been seen that the Lioville operator
could be split in two parts:
N
N
!
!
x i
=
iL =
x
i
i=1
i (x)
= iLH + iLnH
x
i
i=1
Since the Trotter theorem is easily extended to the exponential of the sum of more
than two operators, we could construct the propagator as follows:
(2)
(1)
(2)
exp(iLt) exp(iLnH t/2)exp(iLH t/2)exp(iLH t)exp(iLH t/2)exp(iLnH t/2)

The strategy is to apply the non-Hamiltonian part
of the dynamics as a correction to a Hamiltonian
reference system!
The operator iLnH generally contains a large
number of terms; it is usually subdivided into
simple contributions which lead to a further
factorization of the propagator.
Molecular Dynamics
Many different integration schemes can be derived using the direct translation
technique with different partitions of the propagator. All of them (usually called
Verlet-like schemes) guarantee time reversibility and energy conservation at long
times. Only for pedagogical purposes we introduce here the Verlet Leaprog scheme:
Molecular Dynamics
t2
ri (t) = ri (0) + vi (t/2)t +
Fi (0)
mi
t2
vi (t/2) = vi (t/2)t +
Fi (0)
mi
The velocities and

positions are updated
at different times,
which hinders the
definition of the total
energy!
Molecular Dynamics
t2
ri (t) = ri (0) + vi (t/2)t +
Fi (0)
mi
t2
vi (t/2) = vi (t/2)t +
Fi (0)
mi
1) position translation at time t

2) velocity translation at time t + t/2
The velocities and

positions are updated
at different times,
which hinders the
definition of the total
energy!
get new forces Fi

do i = 1,N
ri ri + vi t
vi vi + Fi t/mi
enddo
Molecular Dynamics
Molecular Dynamics
lim A = !A"
Ergodic hypothesis: trajectory averages of any property are

equal to the ensemble averages obtained from a given
ensemble distribution.
Molecular Dynamics
lim A = !A"

In Hamiltonian systems the ensemble average is generated according to a microcanonical

distribution. In order to generate trajectories which sample other statistical mechanical
ensembles Andersen introduced the use of extended Lagrangians.
Molecular Dynamics
lim A = !A"


The extended Lagrangian formalism consist simply in introducing additional dynamical
variables in the Lagrangian. For example, at constant pressure, the volume of the system can
fluctuate; such fluctuations are modelled by considering the volume a dynamical variable:
Molecular Dynamics
lim A = !A"

L(rN , r N ) =
N
!
mi
i=1
r i r i
!
i<j
u(rij )
Molecular Dynamics
lim A = !A"


L(r , r , V, V ) =
N
N
!
mi
i=1
1 2
u(rij ) + V pV
r i r i
2
2
i<j
Molecular Dynamics
lim A = !A"


L(r , r , V, V ) =
N
N
!
mi
i=1
1 2
u(rij ) + V pV
r i r i
2
2
i<j
kinetic energy
Molecular Dynamics
lim A = !A"


L(r , r , V, V ) =
N
N
!
mi
i=1
1 2
u(rij ) + V pV
r i r i
2
2
i<j
kinetic energy
potential energy
Molecular Dynamics
L(r , r , V, V ) =
N
N
!
mi
i=1
1 2
u(rij ) + V pV
r i r i
2
2
i<j
kinetic energy
potential energy
Molecular Dynamics
L(r , r , V, V ) =
N
N
!
mi
i=1
1 2
u(rij ) + V pV
r i r i
2
2
i<j
kinetic energy
potential energy
This Lagrangian could be interpreted as if we had a N-particles fluid in a container of

volume V which is isotropically compressed by a piston of mass subject to an external
pressure p. The equations of motion of such a system are:
Molecular Dynamics
L(r , r , V, V ) =
N
N
!
mi
i=1
1 2
u(rij ) + V pV
r i r i
2
2
i<j
kinetic energy
potential energy

pi
1 d ln V
dri
=
+ ri
dt
mi
3
dt
dpi
=
dt
N
!
j!=i
N
1 d ln V
rij u (rij ) pi
3
dt
"
1 2 # pi pi
1#
d2 V
rij u! (rij )
2 = p +
dt
V
3 i=1 2mi
3 i<j
Molecular Dynamics
L(r , r , V, V ) =
N
N
!
mi
i=1
1 2
u(rij ) + V pV
r i r i
2
2
i<j
kinetic energy
potential energy

Hamiltonian
part
pi
1 d ln V
dri
=
+ ri
dt
mi
3
dt
dpi
=
dt
N
!
j!=i
N
nonHamiltonian
part
1 d ln V
rij u (rij ) pi
3
dt
"
1 2 # pi pi
1#
d2 V
rij u! (rij )
2 = p +
dt
V
3 i=1 2mi
3 i<j
Molecular Dynamics
L(r , r , V, V ) =
N
N
!
mi
i=1
1 2
u(rij ) + V pV
r i r i
2
2
i<j
The
ensemble
kinetic
energysampled by the
potential energy
trajectory obtained from these
This Lagrangian could be interpreted
we had is
a N-particles
fluid in a container of
equationsasofif motion
the
volume V which is isotropically
compressed by
a piston
of mass subject to an external
isoenthalpic-isobaric
ensemble
(NPH)
pressure p. The equations of motion
of the
such
a system
in which
pressure
is are:
p.
Hamiltonian
part
pi
1 d ln V
dri
=
+ ri
dt
mi
3
dt
dpi
=
dt
N
!
j!=i
N
nonHamiltonian
part
1 d ln V
rij u (rij ) pi
3
dt
"
1 2 # pi pi
1#
d2 V
rij u! (rij )
2 = p +
dt
V
3 i=1 2mi
3 i<j
Molecular Dynamics
A similar approach is used to sample the canonical ensemble (NVT). The method was
introduced by Nos and then improved by Hoover (NH).
LNH = L(r , r , s, s)
=
N
!
mi
i=1
1 2 L
u(rij ) + s ln s
s r i r i
2
2
i<j
2
Molecular Dynamics
LNH = L(r , r , s, s)
=
N
!
mi
i=1
1 2 L
u(rij ) + s ln s
s r i r i
2
2
i<j
2
To get a physical interpretation of this Lagrangian would take a quite involved

derivation...it suffices to mention that the variable s can be interpreted as a scaling factor
of the time step.
Molecular Dynamics
LNH = L(r , r , s, s)
=
N
!
mi
i=1
1 2 L
u(rij ) + s ln s
s r i r i
2
2
i<j
2
To get a physical interpretation of this Lagrangian would take a quite involved

derivation...it suffices to mention that the variable s can be interpreted as a scaling factor
of the time step.
We define
= sps / ; the equations of motion for the NH system are:
pi
dri
=
dt
mi
N
!
dpi
rij u" (rij ) pi
=
dt
j!=i
ds
= s
dt
!N
#
1 " pi pi
L
di
=
dt
i=1 mi
Molecular Dynamics
The NH method is efficient for sampling the canonical ensemble but has the drawback
that the algorithm does not guarantee ergodicity. To solve this problem a chain of M NH
thermostats is usually implemented in the so-called Nos - Hoover chains (NHC).
Molecular Dynamics
The NH method is efficient for sampling the canonical ensemble but has the drawback
that the algorithm does not guarantee ergodicity. To solve this problem a chain of M NH
thermostats is usually implemented in the so-called Nos - Hoover chains (NHC).
pi
dri
=
dt
mi
N
!
p1
dpi
"
rij u (rij )
=
pi
dt
1
j!=i
pk
dk
=
k = 1, . . . , M
dt
k
pk+1
dpk
= Gk
pk
k = 1, . . . , M 1
dt
k+1
G1 =
N
!
pi pi
i=1
mi
1 = dN kB T 2
dN kB T
pk1
kB T
Gk =
k1
k = kB T 2
dpM
= GM
dt
k = 2, . . . , M
k = 2, . . . , M
Molecular Dynamics
One
dimensional canonical harmonic oscillator
!"#$%&'#"(&)"*+,-*")"&-*+,.*/')"&-,)(-&++*0)/
!! "
""
# #! ! $ !
!# !
!"#$%&'"()(*('+
& % !$ "
$ & $!
%
!% #
# !#
,"#$%&'"()(*('+-
& %$$ "
$ # ! ! &$#!
%
!%
$! # !
."#$%&'"()(*('+-
Molecular Dynamics
To obtain the integration scheme for NHC equations of motion the direct translation
technique is used. To this end we need to define the partition of the classical propagator.
Molecular Dynamics
iLNHC = iLr + iLv + iLC
Molecular Dynamics
iLr =
N
!
i=1

vi ri
N
!
Fi
iLv =
vi
m
i
i=1
Molecular Dynamics
iLr =
N
!
N
!
Fi
iLv =
vi
m
i
i=1
vi ri
i=1
iLC =
M
!
k=1
M
M
1
!
!
"
#
vk
vi vi +
Gk vk vk+1
+ GM
k i=1
vk
vM
k=1
Molecular Dynamics
iLr =
N
!
N
!
Fi
iLv =
vi
m
i
i=1
vi ri
i=1
iLC =
M
!
k=1
M
M
1
!
!
"
#
vk
vi vi +
Gk vk vk+1
+ GM
k i=1
vk
vM
k=1
eiLt = eiLC t/2 eiLv t/2 eiLr t eiLv t/2 eiLC t/2
Molecular Dynamics
If M=2, the chain propagator can be split into 5 operators: iLC =
5
!
j=1
iLjC
Molecular Dynamics
5
!
j=1
iLC t
iL5C t/4
=e
iL4C t/8 iL3C t/4 iL4C t/8
iL2C t/2 iL1C t/2
iL4C t/8
iL3C t/4
iL4C t/8
"
"
iL5C t/4
iLjC
Molecular Dynamics
5
!
j=1
iLC t
iL5C t/4
=e
iL2C t/2 iL1C t/2
iL4C t/8
iL3C t/4
iL4C t/8
"
"
iL5C t/4
iLjC
Molecular Dynamics
5
!
j=1
iLC t
iL5C t/4
=e
iL2C t/2 iL1C t/2
iL4C t/8
iL3C t/4
iL4C t/8
"
"
iL5C t/4
subroutine integrate
call chain
call vel_verlet
call chain
iLjC
Molecular Dynamics
5
!
j=1
iLC t
iL5C t/4
=e
iL2C t/2 iL1C t/2
iL4C t/8
iL3C t/4
iL4C t/8
"
"
iL5C t/4
subroutine integrate
subroutine chain
call chain
call vel_verlet
call chain
update thermostat velocities

update thermostat positions
scale particles velocities
iLjC
Molecular Dynamics
According to the statistical mechanical theory of non-Hamiltonian systems we can compute
both the phase space compressibility and its invariant measure:
Molecular Dynamics
(x, t) = x =
N
!
[ri ri + pi pi ] +
i=1
d = exp 1 +
M
!
k=1
M
"
k=2
"
pk
k
+
k
pk
dN pdN rdM p dM
= dN 1
M
!
k=2
Molecular Dynamics
(x, t) = x =
N
!
[ri ri + pi pi ] +
i=1
d = exp 1 +
M
!
k=1
M
"
k=2
"
pk
k
+
k
pk
= dN 1
dN pdN rdM p dM
It has been shown that the resulting distribution function

correspond to the canonical distribution function.
M
!
k=2
Molecular Dynamics
Molecular Dynamics
Total potential energy:
Upol
U = U0 + Upol
!
! Pi Pi
=
Ei Pi +
2
i
i
i
Molecular Dynamics
U = U0 + Upol
!
! Pi Pi
Upol =
Ei Pi +
2
i
i
i
Ei = Tij Pi
Pi = i Ei
Molecular Dynamics
U = U0 + Upol
!
! Pi Pi
Upol =
Ei Pi +
2
i
i
i
Ei = Tij Pi
Pi = i Ei
The dipoles must satisfy the condition that the polarization potential energy is always a
minimum. In MD simulations it can be done following three approaches:
Molecular Dynamics
U = U0 + Upol
!
! Pi Pi
Upol =
Ei Pi +
2
i
i
i
Ei = Tij Pi
Pi = i Ei
The dipoles are computed via

matrix inversion. For big
systems this approach is very
time consuming and is no
longer applied.
Molecular Dynamics
U = U0 + Upol
!
! Pi Pi
Upol =
Ei Pi +
2
i
i
i
Ei = Tij Pi
Pi = i Ei
The dipoles are computed via At each time step the dipoles
are computed iteratively until
self-consistency of the dipole
field (or of the dipoles) is
longer applied.
reached.
Molecular Dynamics
U = U0 + Upol
!
! Pi Pi
Upol =
Ei Pi +
2
i
i
i
Ei = Tij Pi
Pi = i Ei
The dipoles are computed via At each time step the dipoles
are computed iteratively until
self-consistency of the dipole
field (or of the dipoles) is
longer applied.
reached.
It is assumed that the induced

dipoles follow adiabatically the
motion of the nuclei such that
the polarization energy is
always at its minimum.
Molecular Dynamics
Molecular Dynamics
The induced dipoles are treated as additional

dynamical variables that are included in the
Lagrangian. This approach is called on-the-fly
optimization or Car-Parrinello method for
optimization.
Molecular Dynamics
M) =
L(rN , r N , PM , P

optimization.
N
!
1
i=1
mi r i r i +
M
!
1
i=1
iP
i U(rN , PM )
i P
Molecular Dynamics
M) =
L(rN , r N , PM , P

optimization.
N
!
1
i=1
pi
dri
=
dt
mi
N
!
dpi
rij U " (rij )
=
dt
j!=i
Pi
L
d2 Pi
i 2 =
=
+ Ei
dt
Pi
i
mi r i r i +
M
!
1
i=1
iP
i U(rN , PM )
i P
Molecular Dynamics
M) =
L(rN , r N , PM , P

optimization.
N
!
1
i=1
pi
dri
=
dt
mi
N
!
dpi
rij U " (rij )
=
dt
j!=i
Pi
L
d2 Pi
i 2 =
=
+ Ei
dt
Pi
i
mi r i r i +
M
!
1
iP
i U(rN , PM )
i P
i=1
Generalized force acting on dipoles; the iterative

scheme is recovered in the limit of mass equal
to zero;
If the dipoles temperature is low enough,
the dipoles fluctuate around their lowest
energy configuration;
Molecular Dynamics
Some Remarks:
Molecular Dynamics
Some Remarks:
To make sure that the induced dipoles are indeed close to their ground state
configuration, the induced dipoles temperature should be kept low;
Molecular Dynamics
Some Remarks:
at the same time the induced dipoles should be able to adapt
rapidly (adiabatically) to changes in the nuclear configuration, to ensure that
the condition of minimum energy is maintained during the simulation;
Molecular Dynamics
Some Remarks:
to satisfy the above requirements, the dipoles masses should be small!
Molecular Dynamics
Some Remarks:
an optimal value for the dipoles mass would be such that the polarization
relaxation time is on the same order of magnitude as the fastest relaxation in
the system.
Molecular Dynamics
Some Remarks:
an optimal value for the dipoles mass would be such that the polarization
relaxation time is on the same order of magnitude as the fastest relaxation in
the system.
in ordinary simulations, the coupling between induced dipole moments and
translational motion of nuclei leads to heat exchange, causing the nuclei
temperature to decrease, while the dipoles temperature increases until they
are equal; to hinder this problem, a NHC is coupled to the particle positions
and another is coupled to the dipoles;
Molecular Dynamics
Molecular Dynamics
It is known that for many systems we can identify motions on different time scales; for
example if we consider molecules at condensed phase, the intramolecular vibration take
place much faster than translations;
Molecular Dynamics
In typical MD simulations the fastest motion of the system we consider represents one
limit for the time step: the fastest the vibration the smallest is the time step.
Molecular Dynamics
One trick to increase the time step is to use bigger masses; in fact the oscillation
frequency would be smaller by a factor
Mold
Mnew
Molecular Dynamics
One trick to increase the time step is to use bigger masses; in fact the oscillation
frequency would be smaller by a factor
Mold
Mnew
Nevertheless, although statical properties are not affected by this choice, dynamical are
indeed different!
Molecular Dynamics
Another way out of such a bottleneck is to notice that we can partition the total force
on particles in a contribution of a reference and a deviation from it:
Molecular Dynamics
Fi =
del
Fi
ref
Fi
ref
Fi
del
Fi
Fi
Molecular Dynamics
Fi =
del
Fi
ref
Fi
ref
Fi
del
Fi
Fi
If the reference system is chosen such that Fref

is a good approximation to the true
i
force, than the propagation of the system with an occasional correction Fdel
could
i
yield an efficient and accurate scheme;
Molecular Dynamics
Fi =
del
Fi
ref
Fi
ref
Fi
del
Fi
Fi

i
could
i
In particular we can take the fast local vibrational forces as reference; this choice is
convenient because those forces are computationally inexpensive to evaluate while the
slow intermolecular forces are much more demanding;
Molecular Dynamics
Fi =
del
Fi
ref
Fi
ref
Fi
del
Fi
Fi

i
could
i
In particular we can take the fast local vibrational forces as reference; this choice is
convenient because those forces are computationally inexpensive to evaluate while the
slow intermolecular forces are much more demanding;
We define two time steps: t is used for propagating the fast motion, and t is used
for propagating the slow motion;
Molecular Dynamics
We then obtain the following expression for the propagator:
!
!
!
" #
!
"
"&n
"
%
$
t
t
ref t
del t
ref
iL
t
exp
exp(iLt) = exp iLdel
exp
iL
exp iLref
exp
iL
2
2
1
2
2
2
2
Molecular Dynamics
!
!
!
" #
!
"
"&n
"
%
$
t
t
ref t
del t
ref
iL
t
exp
exp
iL
exp iLref
exp
iL
2
2
1
2
2
2
2
ref
iL
N "
!
pi
i=1
ref
+ Fi
mi ri
pi
Molecular Dynamics
!
!
!
" #
!
"
"&n
"
%
$
t
t
ref t
del t
ref
iL
t
exp
exp
iL
exp iLref
exp
iL
2
2
1
2
2
2
2
ref
iL
N "
!
pi
i=1
ref
+ Fi
mi ri
pi
del
iL
N
!
i=1
Fdel
i
pi
Molecular Dynamics
!
!
!
" #
!
"
"&n
"
%
$
t
t
ref t
del t
ref
iL
t
exp
exp
iL
exp iLref
exp
iL
2
2
1
2
2
2
2
ref
iL
N "
!
pi
i=1
ref
+ Fi
mi ri
pi
This operator corresponds to the

propagation of n time steps of the
reference system;
del
iL
N
!
i=1
Fdel
i
pi
Molecular Dynamics
!
!
!
" #
!
"
"&n
"
%
$
t
t
ref t
del t
ref
iL
t
exp
exp
iL
exp iLref
exp
iL
2
2
1
2
2
2
2
ref
iL
N "
!
pi
i=1
ref
+ Fi
mi ri
pi

reference system;
del
iL
N
!
i=1
Fdel
i
pi

propagation of the slow system; it
is applied at both sides to
garantee time reversibility!
Molecular Dynamics
!
!
!
" #
!
"
"&n
"
%
$
t
t
ref t
del t
ref
iL
t
exp
exp
iL
exp iLref
exp
iL
2
2
1
2
2
2
2
ref
iL
N "
!
pi
i=1
ref
+ Fi
mi ri
pi

reference system;
del
iL
N
!
i=1
Fdel
i
pi

This procedure is called reversible reference system propagator algorithm which

acronym is r-RESPA; if there is a wide separation in time scales, then the outer
time step could be large, allowing a large gain in CPU time!
Molecular Dynamics
!
!
!
" #
!
"
"&n
"
%
$
t
t
ref t
del t
ref
iL
t
exp
exp
iL
exp iLref
exp
iL
2
2
1
2
2
2
2
ref
iL
N "
!
pi
i=1
ref
+ Fi
mi ri
pi

reference system;
del
iL
N
!
i=1
Fdel
i
pi

This procedure is called reversible reference system propagator algorithm which

acronym is r-RESPA; if there is a wide separation in time scales, then the outer
time step could be large, allowing a large gain in CPU time!
The algorithm could be easily extended to incorporate motion on more than two
time scales!
Molecular Dynamics
Care must be taken in the choice of time steps because in certain circumstances there
could appear resonance phenomena;
Molecular Dynamics
The propagator is easily translated to an algorithm:
!
!
!
" #
!
"
"&n
"
%
$
t
t
ref t
del t
ref
iL
t
exp
exp
iL
exp iLref
exp
iL
2
2
1
2
2
2
2
Molecular Dynamics
!
!
!
" #
!
"
"&n
"
%
$
t
t
ref t
del t
ref
iL
t
exp
exp
iL
exp iLref
exp
iL
2
2
1
2
2
2
2
subroutine respa (f_ref,f_del)

call vels(f_del)
do i = 1,n
call vel_verlet(f_ref)
enddo
call force(f_ref,f_del)
call vels(f_del)
Molecular Dynamics
!
!
!
" #
!
"
"&n
"
%
$
t
t
ref t
del t
ref
iL
t
exp
exp
iL
exp iLref
exp
iL
2
2
1
2
2
2
2
subroutine respa (f_ref,f_del)
subroutine vel_verlet(f_ref)
call vels(f_del)
do i = 1,n
call vel_verlet(f_ref)
enddo
do i = 1,N
call vels(f_ref)
call pos(v_ref)
enddo
call fast_forces(f_ref)
do i = 1,N
call vels(f_ref)
enddo
call force(f_ref,f_del)
call vels(f_del)
Molecular Dynamics
Molecular Dynamics
In classical mechanics we refer to constraints when it is necessary to take into account
something which limits the motion of the system;
Molecular Dynamics
For example, two beads connected by a rigid rod of length d are constrained to move in
such a way that their distance is constant;
Molecular Dynamics
Holomic constraints are expressed as equations connecting the coordinates of particles;
f (r1 , r2 , . . . , rN , t) = 0;
Molecular Dynamics
f (r1 , r2 , . . . , rN , t) = 0;
The simplest example of holomic constraint is the rigid body:
2
= |ri (t) rj (t)| d2ij =
Molecular Dynamics
f (r1 , r2 , . . . , rN , t) = 0;
The simplest example of holomic constraint is the rigid body:
2
= |ri (t) rj (t)| d2ij =
Holomic constraints are easily included in the Lagrangian:
L(rN , r N ) =
N
!
1
i=1
mi r i r i U(rN )
Nc
!
=1
(rN )
Molecular Dynamics
pi
dri
=
dt
mi
Nc
N
!
!
dpi
"
rij u (rij )
=
= Fi + Gi
dt
r
i
=1
j!=i
Molecular Dynamics
pi
dri
=
dt
mi
Nc
N
!
!
dpi
"
rij u (rij )
=
= Fi + Gi
dt
r
i
=1
j!=i
Constraint force
Molecular Dynamics
pi
dri
=
dt
mi
Nc
N
!
!
dpi
"
rij u (rij )
=
= Fi + Gi
dt
r
i
=1
j!=i
The problem reduces to find the

value of the lagrange multiplier!
Constraint force
Molecular Dynamics
pi
dri
=
dt
mi
Nc
N
!
!
dpi
"
rij u (rij )
=
= Fi + Gi
dt
r
i
=1
Constraint force
j!=i


Since
= 0 we obtain:
t
Nc
N
N
!
!
!
1
1 !

r i r j i j = F M +T = 0
=
i i +
Fi i
t
mi
mi
i=1
i=1
i,j
=1
Molecular Dynamics
pi
dri
=
dt
mi
Nc
N
!
!
dpi
"
rij u (rij )
=
= Fi + Gi
dt
r
i
=1
Constraint force
j!=i


Since
= 0 we obtain:
t
Nc
N
N
!
!
!
1
1 !

r i r j i j = F M +T = 0
=
i i +
Fi i
t
mi
mi
i=1
i=1
i,j
=1
Which formal solution in matrix form is = M 1 (F + T )
Molecular Dynamics
pi
dri
=
dt
mi
Nc
N
!
!
dpi
"
rij u (rij )
=
= Fi + Gi
dt
r
i
=1
Constraint force
j!=i
Since for matrix inversion the exact

solution of the differential equations of
motion is needed, and since in MD we
deal only with finite difference equations,

Since
= 0 we obtain:
this approach fails after few steps because
t
even small errors diverge exponentially!
Nc
N
N
!
!
!
1
1 !

r i r j i j = F M +T = 0
=
i i +
Fi i
t
mi
mi
i=1
i=1
=1
i,j
Which formal solution in matrix form is = M 1 (F + T )
Molecular Dynamics
iterative algorithm (SHAKE/RATTLE):
Molecular Dynamics
iterative algorithm (SHAKE/RATTLE):
I. begin with a system in which all constraints are satisfied within a specified tolerance;
II. evaluate all non-constraint forces on the atoms;
III. move all atoms according to those forces;
IV. Apply the following iteratively:
IV.1. consider each constraint in turn:
IV.1.a. evaluate the constraint equation;
IV.1.b. if satisfied to within tolerance, consider the next constraint, otherwise:
IV.1.c. calculate what the constraint forces should have been at time t so that this
constraint would now be satisfied at new time step;
IV.1.d. move the atoms according to the force evaluated in the previous point;
IV.1.e. consider the next constraint;
IV.2. begin next iteration in which all constraints are considered;
V. Continue until all the constraints are satisfied to within the specified tolerance.
Molecular Dynamics
Few words about the method of constraints to compute free energy differences:
Molecular Dynamics
In the simulation of rare events (such as many reactions) the blue moon ensemle method
allows one to compute the potential of mean force, which can be obtained from the
average force of constraint:
"
#
! 2
H
!
d
F(2 ) F(1 ) =
!
1
Molecular Dynamics
"
#
! 2
H
!
d
F(2 ) F(1 ) =
!
1
Free energy difference along a
given one-dimensional
reaction coordinate.
Conditioned average
in the constraint
ensemble
Molecular Dynamics
"
#
! 2
H
!
d
F(2 ) F(1 ) =
!
1
Conditioned average
in the constraint
ensemble
In MD the statistical average is replaced by the time average over a constrained

trajectory with the reaction coordinate fixed at special values such that:
N
!
N N
(r ) =
(r
, r ) = 0
Molecular Dynamics
"
#
! 2
H
!
d
F(2 ) F(1 ) =
!
1
Conditioned average
in the constraint
ensemble
In MD the statistical average is replaced by the time average over a constrained

trajectory with the reaction coordinate fixed at special values such that:
N
!
N N
(r ) =
(r
, r ) = 0
The free energy difference is evaluated according to this relation:

! 2
! dF
d
F(2 ) F(1 ) =
d !
1
Molecular Dynamics
Molecular Dynamics
F(2 ) F(1 ) =
! dF
d
d !
Molecular Dynamics
F(2 ) F(1 ) =
! dF
d
d !
The problem is reduced to the calculation of the derivative of the free energy with
respect to the constraint; it can be shown that it is easily obtained by computing
unconditioned averages as directly obtained from constrained MD runs:
Z
dF
=
!
d
"
[ + kB T G] !
!
"
Z 1/2 !
1/2
Molecular Dynamics
F(2 ) F(1 ) =
! dF
d
d !
Z
dF
=
!
d
"
[ + kB T G] !
!
"
Z 1/2 !
1/2
Lagrange multiplier as
obtained from the
constrained MD
Molecular Dynamics
F(2 ) F(1 ) =
! dF
d
d !
Z
dF
=
!
d
"
#
N
N
!
1 (r )
Z=
mi
ri
i=1
"
[ + kB T G] !
!
"
Z 1/2 !
1/2
"
#
N
N
2
N
N
!
1
(r ) (r ) (r )
1
G= 2
Z i,j mi mj
ri
ri rj
rj
obtained from the
constrained MD
Molecular Dynamics
F(2 ) F(1 ) =
! dF
d
d !
Z
dF
=
!
d
"
#
N
N
!
1 (r )
Z=
mi
ri
i=1
Weighting factor for the

configurational bias introduced
by the constraint
"
[ + kB T G] !
!
"
Z 1/2 !
1/2
"
#
N
N
2
N
N
!
1
(r ) (r ) (r )
1
G= 2
Z i,j mi mj
ri
ri rj
rj
obtained from the
constrained MD
Correction factor for

blue moon mean
force
Molecular Dynamics
if we consider a simple distance constraint, then:
(rN ) = |ri rj |
Molecular Dynamics
(rN ) = |ri rj |
"
#
N
N
!
1 (r )
= constant
Z=
m
r
i
i
i=1
"
#
N
N
2
N
N
!
1
(r ) (r ) (r )
1
=0
G= 2
Z i,j mi mj
ri
ri rj
rj
Molecular Dynamics
(rN ) = |ri rj |
"
#
N
N
!
1 (r )
= constant
Z=
m
r
i
i
i=1
"
#
N
N
2
N
N
!
1
(r ) (r ) (r )
1
=0
G= 2
Z i,j mi mj
ri
ri rj
rj
!
Z
dF
=
!
d
"
[ + kB T G] !
!
"
= "#!
1/2
Z
!
1/2
Molecular Dynamics
a quite widespread constraint is the so-called coordination number constraint, defined as:
N
(r ) = ni (r ) =
N
!
k!=i
1
1 + exp [(rik rc )]
Molecular Dynamics
N
(r ) = ni (r ) =
N
!
k!=i
1
1 + exp [(rik rc )]
Molecular Dynamics
Fig. 3 Protonation of PO5H32". (a) 91 fs: initial configuration of PO5H32" with one O" in the axial position and one O" in the equatorial position
(black coloured atoms). (b) 127 fs: the axial O" pulls a proton of a neighbouring water molecule towards it. (c) 197 fs: solventsolute proton transfer has occurred and a H3O2" is formed. (d) 800 fs: after the breakup of H3O2" we have PO5H4", 28 H2O, and OH".
surprising that we observe spontaneous deprotonation within
For each, fixed, value of the coordination number a trajectory
N
femtoseconds (Fig. 5d).
of roughly 2 to 3 ps length was computed. In Fig. 4a the blue14
N
N the mean
This dehydration process is in competition with the deprotomoon corrected average constraint
force, i.e.
i
nation reaction we intend to enforce by using coordination
force, is plotted as a function of the coordination
number
for both the axial and the equatorial site. The equilibrium
ik
c
k!
=
i
value of n was determined to be 0.98 in both cases from the trajectory of unconstrained P(OH)5 . In the region just below the
equilibrium value of n we observe a steep rise of the mean force
reaching a maximum at n 0.925. As expected, the restoring
force resisting proton abstraction is significantly higher for
an axial proton than for an equatorial proton, the mean forces
being 286.6 kJ mol"1 and 214.6 kJ mol"1, respectively. With
further decreasing coordination number the mean force is seen
to fall off towards zero and we observe the formation of a
H5O2+ ion (Zundel ion) (Fig. 5a). The smallest value of n
for which a meaningful trajectory could be obtained was 0.2
in the case of the equatorial site and 0.3 for the axial position.
For smaller n the H5O2+ ion breaks up into a hydronium ion
and a water molecule H2OA which has accepted the proton
from the phosphorane and donated another proton to its nearest neighbour. The newly created H3O+ ion is now free to
attack the negatively charged phosphorane. Fig. 5bc illustrates how an axial hydroxyl group of the phosphorane is
protonated turning it into a H2O+ group initially. The
corresponding PO bond is subsequently broken and a neutral
Fig. 4 (a) Mean force of constraint as a function of the coordination
water molecule leaves the phosphorane molecule. Since we are
number n for the axial (K) and the equatorial (S) site; (b) correspondnow dealing with phosphoric acid, H3PO4 , in water, it is not
ing free energy curves obtained by integration of the mean forces.
(r ) = n (r ) =
1
1 + exp [(r r )]
Phys. Chem. Chem. Phys., 2003, 5, 26122618
2615
Molecular Dynamics
Molecular Dynamics

An Introduction To Advanced Molecular Dynamics Techniques

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Molecular Dynamics - Bibliography

Molecular Dynamics - Bibliography

rij u" (rij )

HOW COULD WE COMPUTE THE DYNAMICS USING AN AB-INITIO

exp(iLt) exp(iL2 t/2) exp(iL1 t) exp(iL2 t/2) + O(t3 )

exp(iLt) exp(iL2 t/2) exp(iL1 t) exp(iL2 t/2) + O(t3 )

exp(iL2 t/2) exp(iL1 t) exp(iL2 t/2) + O(tt2 )

acts as a translation operator on

acts as a translation operator on

becomes a translational operator on

These equations constitute

These equations constitute

1) first velocity translation

3) second velocity translation

exp(iLt) exp(iLnH t/2)exp(iLH t/2)exp(iLH t)exp(iLH t/2)exp(iLnH t/2)

The velocities and

1) position translation at time t

The velocities and

get new forces Fi

Ergodic hypothesis: trajectory averages of any property are

Ergodic hypothesis: trajectory averages of any property are

In Hamiltonian systems the ensemble average is generated according to a microcanonical

Ergodic hypothesis: trajectory averages of any property are

In Hamiltonian systems the ensemble average is generated according to a microcanonical

In Hamiltonian systems the ensemble average is generated according to a microcanonical

Ergodic hypothesis: trajectory averages of any property are

In Hamiltonian systems the ensemble average is generated according to a microcanonical

Ergodic hypothesis: trajectory averages of any property are

In Hamiltonian systems the ensemble average is generated according to a microcanonical

Ergodic hypothesis: trajectory averages of any property are

In Hamiltonian systems the ensemble average is generated according to a microcanonical

This Lagrangian could be interpreted as if we had a N-particles fluid in a container of

This Lagrangian could be interpreted as if we had a N-particles fluid in a container of

This Lagrangian could be interpreted as if we had a N-particles fluid in a container of

To get a physical interpretation of this Lagrangian would take a quite involved

To get a physical interpretation of this Lagrangian would take a quite involved

= sps / ; the equations of motion for the NH system are:

& %$$ "

iLNHC = iLr + iLv + iLC

iLNHC = iLr + iLv + iLC

iLNHC = iLr + iLv + iLC

iLNHC = iLr + iLv + iLC

iL4C t/8 iL3C t/4 iL4C t/8

iL2C t/2 iL1C t/2

iL4C t/8 iL3C t/4 iL4C t/8

iL2C t/2 iL1C t/2

iL4C t/8 iL3C t/4 iL4C t/8

iL2C t/2 iL1C t/2

iL4C t/8 iL3C t/4 iL4C t/8

iL2C t/2 iL1C t/2

update thermostat velocities

It has been shown that the resulting distribution function

The dipoles are computed via

It is assumed that the induced

The induced dipoles are treated as additional

The induced dipoles are treated as additional

The induced dipoles are treated as additional

The induced dipoles are treated as additional

Generalized force acting on dipoles; the iterative

If the reference system is chosen such that Fref

If the reference system is chosen such that Fref

If the reference system is chosen such that Fref