Molecular Dynamics Simulations

Devvi Sarwinda
Computational Chemistry
FMIPA-UI 2016

Outline
Basic Concepts in MD
Building Model and Visualization

Why Molecular Dynamics?

1. Scale: Large collections of interacting particles that cannot
(and should not) be studied by quantum mechanics .
Classical limit?

Quantum
~500,000
atoms

~115 nm

~25 nm

~2,000,000
atoms

2. Dynamics: time dependent behavior

and non-equilibrium processes.
3. Atoms and molecules interact in certain period based
on Physics Laws

Statistical Ensembles

, , =

Q is called the
Canonical Partition Function.
A , , =
, , =
, , =
, , =

microcanonical
grand canonical

Isothermal-isobaric

A Few Theoretical Concepts

Classical configuration Integral

1 = 1 , 1 1 + (2 )
2 = ? ? ?

The van Der Waals Equation

Potentials modeling pairwise interactions.

Hard sphere Potential

Lennard-Jones Potential

Molecular Dynamics: Nuts and Bolts

Particles (atoms and molecules): non-reactive, stable species (generally).
trajectories determined by solving Newtonian equations of motion
Forces on particles due to molecular mechanics force fields.
Basic Force Field components

+ other possibilites (implicit solvent, external potentials)

Common types of force fields

United Atom

Includes explicit H atoms

All Atom
Partial charges on most atoms
Most atoms
uncharged,
Exceptions for
O-H groups
etc.

Tip4p

(graphic: sklog Wiki)

Coarse Grain
Beads include large
functional groups.

SPC
/2

http://dx.doi.org/10.1063/1.4863329

1 (nonpolar) Martini
water bead
represents 4 water
molecules

(http://espressomd.org)

Force Field Parametrization

Force Fields are largely empirical
You get so many parameters: Make them fit
experiment!

Ab initio calculations can be used

How does one get charges?

Transferability
Want to model systems containing mixtures of
particles which were parameterized (want parameters
to transfer to new systems). Possible if all
parameters derived in same way

Molecular Modeling
For each atom in every molecule, we need:

How do the dynamics happen?

Forces on each particle are calculated at time t. The forces provide
trajectories, which are propagated for a small duration of time, t,
producing new particle positions at time t+ t. Forces due to new
positions are then calculated and the process continues:

The **basic** idea

What is the Potential?

A single atom will be affected by the potential
energy functions of every atom in the system:

V ( R) Ebonded Enonbonded

How do the dynamics happen?

Verlet algorithm

Velocity Verlet algorithm

Leap-Frog algorithm

Verlet Algorithm
Pros:
Simple & Effective
Low Memory & CPU Requirements (dont need to
store velocities or perform multiple force
calculations)
Time Reversible
Very stable even with large numbers of interacting
particles
Cons:
Not as accurate as RK
We never calculate velocities!
(when would we need them?)

Obtaining Velocities
We can estimate the velocities using a finite difference:

1
2
v(t )
[r (t t ) r (t t )] O(t )
2t
This has a second order error, while our algorithm has a
fourth order error
There are variations of the Verlet algorithm, such as the
leapfrog algorithm, which seek to improve velocity
estimations.

Molecules in Solution
In real situations, a molecule is rarely
isolated. In biological systems,
proteins, RNA, and DNA are immersed
in a sea of water molecules
To accurately portray the effect of the
solvent molecules on a system, the
solvent molecules must be free flowing
How do we establish computational
boundaries while keeping a realistic
solvent simulation?

How do the dynamics happen?

What is a suitably short time step?
Must be significantly shorter than
the fastest motion in your
simulation:

What is frequency of C-H stretch. O-H stretch?

Adequately
Short Time
step

Normal
restoring
force

Huge restoring
force:
simulation
crashes
Time step
Too long
Minimum time step depends on what you are
monitoring. At least, simulation must be stable.
Constraint algorithms: Shake, Rattle, LINCS

Cuttoffs and Boundaries

Do we use the entire configuration integral?

Cutoff (modified cutoff) radii

For L-J, 2.5
Long-range electrostatics
Ewald Sums

Graphic credit: http://beam.acclab.helsinki.fi/~koehenri

How do you keep your particles from

drifting
out of the cell?
1.Create some type of a wall
2. PERIODIC BOUNDARY CONDITIONS
Whats the maximum cutoff?

Graphic credit: http://server.ccl.net/cca/documents/molecularmodeling/node9.html

Live Demo