martin Flashcards
what are multi scale methods?
When small scale and large scale calculations are run simultaneously
what are continuum methods?
only dielectric medium, no atoms
what is a force field?
Sum of intramolecular and intermolecular interactions
what is the born oppenheimer assumption?
Electrons move faster than nuclei so the nuclei can be considered as stationary and the electrons are moving in the constant potential energy field.
explain the molecular mechanic explanation why eletcron electron interactions can be ignored?
electrons move so fast that we only see an average distribution of electrons around a nucleus. If we are only interested in nuclei positions we can consider only nuclei - nuclei interactions.
`give the equation for hookes law?
E = 0.5K (X - Xo)^2
what is storic energy?
The amount of strain in a molecules bond length
what is the equation for force relating to hookes law?
F = -K (x-xo)
what happens is x= xo
x>xo
x < xo
when x and xo are = the atoms are in ideal positions
when x is greater than xo then F<0 and pushes atoms to left .
when x is less than xo then F > 0 and force drives atom to right
what are the advantages of quantum mechanics?
Rigorous description of ee and e nuclei interactions
Abinito- no experimental input
can cope with new structures
only method for electronic properties
disadvantages of quantum mechanics?
slow
to solve Schrodinger equation needs high accuracy of qm
disadvantages of quantum mechanics?
slow
to solve Schrodinger equation needs high accuracy of qm
advantages of molecular mechanics?
v fast
allows dynamics of molecules to be studied
applicable to large systems
if properly paramertised then can be as accurate as QM
what are the disadvantages of molecular mechanics?
parameters need to be chosen
cant cope with new structures
QM of experiment needs to be done first
applicable to describing molecules not electronic properties
when to use quantum mechanics?
for electronic properties
MO, excited states, light absorptions, bond rearrangement and charge transfer
when to use to molecular mechanics?
large systems, large molecules (Bimolecular), dymanics of molecules, molecules in solution, organic inorganic interfaces and metal organic molecules.
what the three bending terms?
Stretch, bending and torsional
what is the equation for steric energy?
E = Estretch + Ebend + Etorsion
name the three out of plane terms?
Non planar molecules
Cross terms - bond deformations affect electron distribution
stretch bend vibrations - these are usually small so not used in force fields
give all the oxygen atom types
O alcohol, O ether, O in C=O in cooh , C-O in COOh
give all the nitrogen atom types
N sp3 - Nh3 or NHR2
N sp2 - 2 atoms bonded
N sp3 - 1 atom bonded
give all the sulphur atom types
-s- sulfide s=o sulfoxide si - silane s+ - sulfonium So2 - sulfone
what is the overall equation for Einter interactions?
Eelec + Evdv + Eh-bond
at large distances dipole dipole interactions can be ignored, why?
1/R3 falls to zero more faster than 1/R
give the lennard jones potential and what is it used to describe?
Non bonded interaction
r = distance between atoms
Ro - the distance where the interaction energy = 0
give the buckingham potential
Ae-br - c/r6
why is water a special case?
H (sigma + charge), O and lp
different force field have been developed
format uses lennard jones and electrostatic potential
describe the parameter fitting procedure?
- choose reliable value of molecular properties
- choose initial values of FF parameters
- use these values to calculate target properties
- are the desired properties produced (if no update parameters and go back to 3.)
- parameter fitting complete
- run calculation
true or false: you can take parameters from one force field and paste them into another force field
false
describe the potential energy curve?
E vs r(ang) which goes through a minimum
describe the potential energy surface?
Polyatomic molecules
Vertical axis is energy and horizontal is internal coordinates = 3N-6
as molecules have many internal coordinates the PES is plotted in many dimensions which is often difficult and hard to obtain
what are saddle points and which is the most interesting?
where they are minima in one direction but maxima in another direction, the most interesting is the transition state where it is a minima in all directions but 1
what’s the difference between global and local minima?
The global minima is the deepest minimum and is most stable
describe the process of conformational search to find the energy minima of a diatomic molecule?
Choose a grid of r values
find E(r) for each value of r
plot E vs r
describe the process of conformational search to find the energy minima of a polyatomic molecule?
1-3 internal coordinates
define grid values for these coordinates
calculate energies at each point of this grid
plot as a contour plot or 3D plot
what are the advantages and disadvantages of conformation search in finding the minima?
Find all minima including global and local
easy to automate and analyse
slow
certain coordinates may be important in different conformation, therefore, some minima may be missed if bad set of coordinates chosen
what are gradient based methods set on?
The potential energy as a function of all the internal coordinates
what does the gradient of energy signify?
1st derivative of energy wrt all internal coordinates
what does the gradient tell you?
How fast the energy decreases and what direction is the fastest decrease
for 1D grad (Eq) = -force
poly - gradient is a column of value. forces on all atoms
Describe what hessian is?
2nd derivative of energy
physical meaning = force constant K
it is the curvature of parabola or the curvature of PES
describe the steepest descent method?
- choose a suitable starting structure
- calculate gradient —-> find the steepest descent
- make a step in that direction
- repeat steps 2 and 3 until convergence is reached
what are the disadvantages and advantages of steepest descent method?
slow compared to more sophisticated methods especially if PES is narrow
fast compared to conformation search
robust - finds minima
describe the conjugate gradient method?
uses information on the gradient from previous steps, therefore, is a more efficient direction towards the minima
what are the advantages and disadvantages of the conjugate gradient method?
fast and efficient. is less efficient if close to the minimum
which minima do conformation search, PEs and gradient methods find?
local minima
finish this sentence: MD is a computational approach…..
that simulates the movement of atoms. MD simulations overcome potential energy barriers and explore various energy minima.
how does MD work?
Approach: 1. Construct several starting structures. 2. Choose an appropriate force field. 3. Run molecular dynamics (MD). 4. Find the lowest-energy structure from several independent MD runs
how are accelerations calculated in the verlet algorithm?
via newtons law a= F/m
How are velocities calculated using the verlet algorithm?
give equation
what are the drawbacks of the verlet algorithm?
Positions at t and Δt need to be known before the start of the simulation.
need to calculate the difference of large terms x(t) and x(t+Δt) which is source of error
how to improve the verlet algorithm and what is the advantage of it?
calculate new positions via velocities and accelerations.
calcite forces and accelerations at (t+Δt) and then velocities calculated in two steps:
1/2 t using v(t+0.5Δt) = v(t) + a(t) x 1/2Δt
then at a(t+Δt) by v(t+Δt) = v(t+1/2Δt) + a(t+ Δt) x 1/2Δt
do not need to store previous coordinates meaning that a lower memory is required
what is the ergodic theorem?
The time average of an observable property is the same as the ensemble average of the same property.
what is the ensemble average?
a measurement which is done simultaneously on a large number of systems
how many times are time average measurements made?
many times - ideally infinite times
how are macroscopic properties measured?
can determine a macroscopic property by observing the coordinated and momenta of each atom
what does the choice of ensemble depend on?
The parameter which is kept constant
describe the NVE ensemble
(Microcanonical)no. of molecules, volume and total energy kept constant. copies of system do no exchange energy with each other.
describe the NVT ensemble?
(canonical or isochoric -isothermal) constant no of molecules, volume and temp. this is a realistic situation. a thermostat is needed to maintain constant temp
describe the NPT ensemble
(isobaric- isothermal) constant no of molecules, pressure and temp. realistic situation for high gases or high pressured systems. a mechanism is needed to maintain constant temp and pressure.
describe the µVT ensemble?
(grand canonical) the chemical potential is kept constant but N varies.
infinite reservoir of molecules. this is not used in MD
which ensembles are used in MD and which for macroscopic properties?
all of them are suitable for macroscopic properties.
NVT and NPT
what are the drawbacks with MD simulations of liquids?
finite volume and surface of cluster behave differently from the bulk.
how does a periodic box work for MD simulations of liquids?
The cell is surrounded on all sides by identical cells. Each molecule interacts with its neighbours both in its in cell and with image cells, therefore, there is no surface and an infinite volume of liquid.
give the procedure for setting up and running MD simulations?
choose an appropriate force field build several starting structures choose simulation parameters -time step -length of simulation - ensemble - thermostat run MD simulation analyse results for serveral simulations
what information is obtained from MD?
structure and dynamics of molecules, conformations of molecules?
MD can be applied to…..
liquids, solutions and solid liquid interface
what does RDF tell you?
tell us how many particles there are at a distance r. within a thin layer r and (r+Δr) for some randomly chose particle
how is simulated annealing used in MD?
Changes to structures are either rejected or accepted depending on whether they lower the energy of the system
What is the process of simulated annealing combined with MD?
Starting temp chosen and the starting velocities corresponding to this temp are assigned to atoms
atoms move according to newtons` law of motion
atoms have high velocities and therefore high KE so are able to overcome potential energy barriers
The systems stay in one minima
what are the disadvantages and advantages of Sim anneal?
guaranteed to find global minima if cooling is done infinitely slowly
may still get stuck in local minima
how does metadynamics ensure that the sytems doesn not get trapped in the local minima?
History dependent potential is constructed
explored minima from PES is filled with guassian functions so that they are not revisited again
describe the process of meta dynamics?
- select an appropriate collectibe variable s(x)
- vary the value of this collective using MD
- at each step (t) and each coordinate calculate the gaussian function
- add all the gaussian functions to find the total potential at coordinate s(x)
the value of s(x) visted the most has the largest value of the potential and is therefore the global minima
how does the monte carlo method follow the evolution of a system?
Trying and accepting (or rejecting) randomly chosen moves of particles
Describe the process of the monte carlo method?
- create starting distrubution of N particles and define the laws that controls particle interactions and chose temp
- create a list of possible moves
- choose a move at random
- calculate the energy change
does this lower the energy of the system - if yes then accept and repeat steps 3-5, if no then accept with a probablility and repeat steops 3-5
give the kinetic monte carlo method?
- first step as the monte carlo + set t=o
- create a list of moves and barriers for these moves for the N particles. calculate the sum of all rates
- choose move at random
4.carry put move - Generate another random number r2
- Update the time as t = t + Δt, where Δt = ln(1/r2
)/R
repeat from step 2
