MOLECULAR STATICS

PRINCIPLE OF THE METHOD

The potential energy of a system of N particles, E p = E p (r1 ,r2 ,.....,rN ) , is minimized
with respect to their positions ri (and, possibly, some other internal coordinates).
After an initial configuration has been specified, the positions of particles are adjusted
using an iterative computational method until the minimum energy configuration is
attained. It should be emphasized that E p , which is a function of 3N variables (in three
dimensions), may possess a number of minima. Which of them is found depends on
both the initial configuration and the method of energy minimization.

No method guarantees that the lowest energy minimum will be found.

MINIMIZATION ALGORITHMS
All methods of the minimization of the potential energy pursue the following route: If in
the mth iteration the system of particles is described by position vectors ri(m ) then in the
(m+1)th iteration the position vectors are
ri(m +1) = ri(m ) + !ri(m )

(MS1)

where !ri(m ) is determined so as to decrease the potential energy E p (r1 ,r2 ,.....,rN ) .
Different molecular statics (MS) methods of relaxation differ in the way !ri(m ) is
determined.

Steepest descent the simplest method

In the first order (linear) approximation a small displacement !ri of an atom i leads to
the energy change

"E p #
# !ri
#=1 "ri
3

!E p = $

(MS2)

where !ri is the component of the vector !ri . This is the Taylor expansion to the
first order. The right side is the scalar product of the vectors grad r E p and !ri and
i

thus the decrease of the energy will be the biggest when !ri is in the direction of

! grad r E p . Physically, ! grad r E p is the force, Fi , acting on the particle i. The

i

steepest descent minimization algorithm 'follows' the gradient of E p (forces on atoms),

i. e. the position vectors ri are being adjusted in proportion to this gradient (forces) at
any given iteration.
In the mth iteration the force acting on the particle i is

Fi(m) = !grad r E p r1(m!1) ,r2(m!1) ,....,rN(m!1)

i

(MS3)

and, therefore, we take

(m)

( m)

!ri = "Fi
(MS4)
where ! is a numerical factor chosen to optimize the efficiency of the procedure and
ensure at the same time convergence of the routine. may remain the same in all
iterations or may be adjusted during the relaxation process. There is no mathematical
rule how to determine the best and this constant is found by trial and error. The
precision with which the minimum is found has to be determined in the calculation. In
order to determine whether the minimum has been reached we follow:
1. The energy of the system and consider the relaxation calculation complete if the
change of the energy from iteration to iteration is below a chosen limit. Frequently,
near the minimum the energy does not decrease monotonously but oscillates.

Energy

2. Magnitude of forces on all atoms is below a set limit. Usually we determine the
maximum force found in the relaxed block and require that the magnitude of this
maximum force has to be below a chosen limit.

Potential energy

Minimum energy

Number of iterations

The dependence of the potential energy on the number of iterations when the energy
decreases monotonously.
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Energy

Potential energy

Minimum energy

Number of iterations

The dependence of the potential energy on the number of iterations when the energy
decreases in an irregular oscillatory manner.
An important hint: During the calculation of forces (energies) you should use the
neighbor list. However, since the atomic configuration changes during the calculation
the neighbor list needs to be updated from time to time. Exactly how often cannot be
said but at the beginning of the calculation the best is to do it after every 50 iterations.

Other methods of minimization of the potential energy

More sophisticated minimization routines provide algorithms for the most efficient
choice of !ri which is then not necessarily parallel to Fi . Such routines are commonly
found in libraries of subroutines.
Newton's method: Use of second derivatives
Taking the Taylor expansion of E p to the second order, i.e. approximating the function
E p locally by a quadratic function, we get
N

!E p = "$ $

i= 1 # = 1

Fi# !ri#

1 N 3
#
%
+ $ $ H #,%
i, j !ri !rj
2 i,j= 1 # ,%=1
3

(MS5)

where the matrix

$& ! 2 E p (&
H =% " #)
(MS6)
&' !ri !rj &*
is the 3N dimensional matrix called Hessian matrix. We now seek such !ri that leads
to the maximum negative value of !E p . The necessary condition for maximization of
!E p is

!"E p
!"ri#

= 0 , which gives

!Fi"

#
+ $ $ H ",#
i, j %rj = 0

(MS7.1)

j= 1 #= 1

This equation can be written in the matrix form as

F = H!R

(MS7.2)

{ } , F the 3N dimensional
!

where R is the 3N dimensional vector with components ri

{ }
!

vector with components Fi and R the 3N dimensional vector with components

!ri" , which are the steps in the procedure. (MS7.2) is a set of 3N linear equation that
can be solved for steps !ri" for which the fastest relaxation will be attained.
However, evaluation of the matrix H and its inversion represents a very substantial
computational effort and this could render this approach less efficient than the simple
steepest descent that does not necessarily choose the most efficient values of !ri . A
major advancement of this algorithm was the development of methods of updating the
"1
matrix ! without re-calculation and inversion of the matrix H. The most commonly
used is the Fletcher-Powell algorithm, also called the variable metric method (R.
"1
Fletcher and M. J. D. Powell, Computer J. 6, 16, 1963), in which ! = S in the
(m +1)
(m )
(m+1)th iteration, S
, is determined approximately on the basis of S
from the
previous mth iteration. In the mth iteration we determine the new displacement

!R ( m ) = "S (m ) F ( m )
(MS8a)
(m)
( F is the vector of forces in the mth iteration and is a parameter chosen for fastest
convergence) and calculate the new positions of atoms used in the (m+1)th iteration
R ( m +1) = R ( m ) + !R ( m )
In the Fletcher-Powell algorithm the matrix S is updated as follows

(MS8b)

(m +1)

=S

(m)

(S
!

(m )

)(

) ! (#R
)
( #R

" #F (m ) " #F T ( m ) S( m )

(m )

#R T ( m )

).
)

(MS9)
T (m)
S #F ( m )
#F (m )
Here the letter T indicates the transpose of the corresponding matrix (vector) and
!F ( m ) = F (m +1) " F (m ) , where F ( m +1) is the vector of forces in the (m+1)th iteration.
(m +2)
The new positions of particles, R
, that are used in the (m+1)th iteration are,
similarly as in (MS8a,b)

( #F

T (m) (m)

R ( m +2) = R ( m +1) + !R (m +1) where !R ( m +1) = "S ( m +1) F ( m +1)

2

A problem, may still be the storage of the matrix S since it has dimensions 9N . This
becomes significant for large systems of particles.
Standard subroutines of this method are available in various libraries and are usually
called VARIABLE METRIC METHOD.

Conjugate gradient
In this method the displacements of atoms, !ri , are not in the directions of the forces
(gradients). In general, in the (m+1)th iteration the directions of the displacements are
not determined only on the basis of the forces calculated in the mth iteration but also
using values of the forces found in previous iterations. This is carried out as follows:

{ } is written as
!

The increment of the 3N dimensional vector R = ri

3N

!R = $ " ! #!

(MS10)

! =1

where !! are 3N vectors in the 3N dimensional space that have been gradually
constructed in the previous 3N iterations (P. R. Adby and M. A. H. Dempster:
Introduction to Optimization Methods, Chapman & Hall, London, 1974).
In the first iteration !1 = F (1) , where F is the 3N dimensional vector of forces
evaluated in the first iteration, and all other vectors !! .for ! > 1 are set to zero. Thus, at
this point the displacements are parallel to the forces as in the steepest descent method.
In the second iteration the vector !2 is constructed as !2 = F ( 2) , similarly as in the first
iteration; all other vectors !! , for ! > 2 are set to zero. In the following iterations the
recursive formula
(1)

!m = F

(m)

F T ( m " 1) F (m " 1)
+ T ( m " 2) (m " 2) !m "1
F
F
5

(MS11)

is used to construct gradually additional vectors !! ; the letter T denotes the transpose
of the corresponding vector. Thus in every iteration, m, a new vector !m is added until
3N vectors have been constructed in the first 3N iterations. At this point these 3N
( 3N +1)
vectors are used to determine !R
in the 3N+1 iteration according to equation
(MS10). When the number of iterations, M, is larger than 3N, then 3N vectors
( M +1)
constructed in the previous 3N iterations are used in determining !R
in the M+1
iteration, again according to equation (MS10).
This method is in many cases more efficient than the steepest decent and standard
subroutines of this method and its variation are available in libraries. However,
similarly as the variable metric method, it may become inefficient for very large
numbers of particles.
Standard subroutines of this method are available in various libraries.

Problems and drawbacks of the MS methods

No algorithm can guarantee that the global minimum is found. The minima found
are always local minima and in complex systems it is likely that relaxations become
trapped in a variety of local minima. However, this may also be advantage if metastable
states are of interest. Hence, a number of starting configurations need to be used to test
the uniqueness and/or possible multiplicity of relaxed structures. When choosing
starting configurations one has to use physical intuition and insight relevant to the
problem studied.
The steepest descent method is most likely to converge to the local minimum nearest to
the starting configuration. The variable metric and conjugate gradient methods are
more likely to bypass shallow local minima but, as any minimization technique, cannot
guarantee the global minimum.
Important warning:
The symmetry of the starting configuration may be preserved throughout the calculation
although it may be the change in the symmetry that is of principal interest. The reason
is that any symmetry of the structure is reflected in the symmetry of the forces Fi . This
can be avoided by removing the symmetry from the starting configuration, for example,
by displacing the atoms randomly away from the positions corresponding to the
symmetric configuration.
It is recommended not to calculate all the forces and then shift all the atoms at
once. This way one preserves the symmetry of the previous iteration. In the
steepest descent the best is to calculate the force on an atom, shift it, and then move
to another atom
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