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MD SIMULATION
Molecular Modeling and Drug Design
Dr. Puneet Kacker
www.puneetsclassroom.in
MD Simulation: Introduction
One of the principal tools in the theoretical study of biological molecules
Calculates the time dependent behavior of a molecular system
Provides detailed information on the fluctuations and conformational changes of proteins and nucleic acids
Used to investigate the structure, dynamicsand thermodynamics of biological molecules and their complexes
Reading Material: CHARMM Theory of MD Simulation
Time Scales Vs. Biological Process
ApplicationsProtein stabilityConformational changesProtein foldingMolecular recognition: proteins, DNA,
membranes, complexesIon transport in biological systems
Drug Design & Structure determination (X-ray and NMR)
Thermodynamics and Kinetics
Historical Background
First introduced by Alder and Wainwright by study of hard sphere interactions (1957) Rahman carried out the first simulation
using a realistic potential for liquid argon (1964)First protein simulations by McCammon
appeared in 1977 with the simulation of the bovine pancreatic trypsin inhibitor (BPTI)
Statistical MechanicsThe conversion of microscopic information
(e.g. atomic positions and velocities) to macroscopic observables (e.g. pressure, energy, heat capacities) requires statistical mechanics
Statistical mechanics provides the rigorous mathematical expressions that relate macroscopic properties to the distribution and motion of the atoms and molecules
Cont…
Relation??
Statistical Mechanics
Some DefinitionsThermodynamic state: of a system is usually
defined by a small set of parameters, e.g. the temperature– T, the pressure– P, and the number of particles– N
Mechanical or microscopic state: of a system is defined by the atomic positions– q, and momenta–p; these can also be considered as coordinates in a multidimensional space called phase space
Ensemble: is a collection of points in phase space satisfying the conditions of a particular thermodynamic state
An EnsembleAn ensemble is a collection of all possible systems which have different microscopic states but have an identical macroscopic or thermodynamic state.
There exist different ensembles with different characteristics
Classical MechanicsMD simulation method is based on Newton’s
second law of motion
Fi is the force exerted on particle i, mi is the mass of particle i and ai is the acceleration of particle i
Integration AlgorithmsThere is no analytical solution to the
equations of motion; they must be solved numerically
Numerous numerical algorithms have been developed for integrating the equations of motion– Verlet algorithm– Leap-frog algorithm– Velocity Verlet– Beeman’s algorithm
Setting up and Running MD Simulations
Potential Energy Function
Potential Energy is the energy of the object or a system due to the position of the body or arrangements of particles of the system
Some Function
InputAtomic Positions
OutputEnergy
Force FieldsBiological systems involve many atomsQuantum Mechanics not a feasible
methodPEF* are less computationally demandingNumerous approximations are introduced
which lead to certain limitationsProvides a reasonably good compromise
between accuracy and computational efficiency
*Potential Energy Functions
Cont…Often calibrated to experimental results
and quantum mechanical calculations of small model compoundsTheir ability to reproduce physical
properties measurable by experiment is testedThe development of parameter sets is a
very laborious task, requiring extensive optimization
Most commonly used potential energy functions
AMBER (Assisted Model Building with Energy Refinement)
CHARMM (Chemistry at HARvard Macromolecular Mechanics)
GROMOS (Groningen Molecular Simulation)
OPLS (Optimized Potentials for Liquid Simulations)/AMBER force fields
Force Field LimitationNo drastic changes in electronic structure are
allowed, i.e., no events like bond making or breaking can be modeled
SolutionMixed quantum mechanical - molecular
mechanical (QM/MM) method
Molecular Mechanics (MM)
Quantum Mechanics (QM)
The CHARMM Potential Energy Function
The energy, E, is a function of the atomic positions, R, of all the atoms in the systemAtomic Positions are usually expressed in
terms of Cartesian coordinates
Describes the bonds, angles and bond rotations in a molecule Describes the interactions between
nonbonded atoms or atoms separated by 3 or more covalent bonds
Ebonded
The Ebonded term is a sum of three terms:
1 2 3
Ebond-stretch
A harmonic potential representing the interaction between atomic pairs where atoms are separated by one covalent bond
Force constants Kb are specific for each pair of bound atoms, i.e. depend on chemical type of atoms-constituents
Ideal bond lengthForce constants
Values of force constant: from infrared stretching frequencies or from QM calculations. Values of bond length: from high resolution crystal structures or microwave spectroscopy data.
Ebond-bend
Associated with alteration of bond angles θ from ideal values θo
Kθ depends on chemical type of atoms constituting the angle
Ideal angle
Erotate-along-bond
Models the presence of steric barriers between atoms separated by 3 covalent bonds (1,4 pairs)
The motion associated with this term is a rotation, described by a dihedral angle and coefficient of symmetry n=1,2,3), around the middle bond
Function is assumed to be periodic and is often expressed as a cosine function
Coefficient of symmetry n=1,2,3)
Enon-bonded
Non-bonded interactions has two componentsSome other potential functions also include an
additional term to account for hydrogen bonds
Eelectrostatic
The electrostatic interaction between a pair of atoms is represented by Coulomb Potential
Effective dielectric function for the medium Distance between two
atoms having charges qiand qk
Evan-der-Waals
One of the most important interactions for the stability of the biological macromolecules
Modelled using the Lennard-Jones 6-12 potentialExpresses the interaction energy using the atom-type
dependent constants A and C
Force Field Limitations Fixed set of atom types for parameterizationAliphatic carbon atom in an sp3 bonding situation has different
properties than a carbon atom found in the His ring An approximation introduced to decrease the computational
demand is the pair-wise additive approximationThe simultaneous interaction between three or more atoms is
not calculated, so certain polarization effects are not explicitlyincluded in the force field
Potential energy function does not include entropic effectsE calculated as a sum of potential functions does not
necessarily correspond to the equilibrium, or the mostprobable state
MD Simulation Movies
MD Simulation Output
MD Simulation
Atomic Coordinates and Velocities
Analysis
X-axis
Y-axis
Conformations
Prop
erti
es o
f Int
eres
t
All
Atom
RM
SDPo
tent
ial E
nerg
yRa
dius
of G
yrat
ion
MD Simulation Packages
AMBERhttp://ambermd.org/
GROMACShttp://www.gromacs.org/
NAMDhttp://www.ks.uiuc.edu/Research/namd/
MD Simulation Analysis Packages
XMGrace (Plotting Tool)http://plasma-gate.weizmann.ac.il/Grace/
VMD (Trajectory Visualization and Plotting Tool)http://www.ks.uiuc.edu/Research/vmd/
Thanks!!
www.puneetsclassroom.in