Hands-on Exercise 3 Molecular Dynamics Simulations

Computational Chemistry in Chemical Engineering
stlin@ntu.edu.tw 2009
<strong>Hands</strong>-on Exercise 3
Molecular Dynamics Simulations
1.General MD procedure
2.Force Field Options in MS 4.4
3.Energy Minimization
4.Dynamics Simulations
5.Analysis of MD results
6.Continue from a previous simulation run
7.Create Animation
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1. General MD Procedure
A complete molecular simulation involves 5 steps
1. Model Building
• create the molecular model of interest
2. Selection of an appropriate Force Field
• simulation results may heavily depend on FF
3. Model Refinement
• perform energy minimization to remove VDW
repulsions in the initial structure
• equilibrate the model at the desired state (T,P or T,V)
with sufficient dynamics simulations
4. Dynamics Simulations
• production runs
5. Result Analysis
• calculation of properties
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2. Force Field options in Materials Studio
There are two MD programs in Materials Studio
1. Discover
2. Forcite
FF selection in Discover:
Modules → Discover → Setup
FF selection in Forcite:
Modules → Forcite → Calculation
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Force Field Parameters
Force Field
Forcefield types
Atomic charges
Accuracy
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Examine Force Field Parameters
Modules → Forcite → Forcefield Manager
select a FF
add to the
project
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1. display
document
3. additional
settings
2. interaction
parameters
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3. Energy minimization using Forcite
Modules → Forcite → Calculation → Setup → Geometry Optimization
medium
accuracy is
usually
sufficient
cell shape
changes if
checked
too many
iterations may
take too much
time
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useful to use motion groups
in initial minimization
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Define Motion Groups
Modify → Motion Groups
Note: Use undo or delete to
remove Motion Groups
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Recap on Energy Minimization (Geometry Optimization)
1. Choose a force field (check atom type, atomic charges)
[Note that it is important to check if net charge of your
model is zero]
2. Choose convergence tolerance (when to stop the
minimization) and maximum iteration steps (stop no
mater what)
3. Whether to optimize the cell parameters (cell lengths and
angles)
4. Whether to keep some molecules rigid during the
geometry optimization
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4. Dynamics Simulation using Forcite
Modules → Forcite → Calculation → Setup → Dynamics
ensemble
initial atom velocity
dynamic temperature
dynamic pressure
integration step
simulation length
output frequency
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T control method
P control method
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Recap on Dynamics Simulations
1. Choose a force field (check atom type, atomic charges)
[Note that it is important to check if net charge of your
model is zero]
2. Make sure the structure is stable (either previously
energy minimized or having dynamics simulation
performed)
3. Set simulation parameters (ensemble, initial velocity,
dynamics temperature and thermostat, pressure and
barostat, integration step, simulation length, output
property and frequency)
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Exercise:
1. Create a 3D periodic cell containing 16 water molecules
2. Assign atomic charges: -0.82 on oxygen and +0.41 on hydrogen
3. Choose the Dreiding forcefield and perform energy minimization
4. Choose the Dreiding forcefield and Perform NPT dynamics for
100 ps at T=300 K, P= 10 atm.
5. Redo the Dynamics simulation using the COMPASS forcefield
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5. Analysis of MD Results
Basic properties you may obtain from doing MD Simulations
1. Energetic Properties: valence energies (bond, angle, torsion,
inversion), nonbond energies (vdW, Coulomb), potential, kinetic,
and total energies, Hamiltonian, etc.
2. Mechanical properties: density, pressure (stress)
3. Transport properties: diffusivity, thermal conductivity, viscosity
4. Electrical properties: dielectric constant
5. Structural properties: IR, radial distribution function, X-ray
diffraction, neutron diffraction, electron diffraction
6. Thermodynamic properties: adiabatic compressibility, isothermal
compressibility , thermal pressure coefficient, gruneisen parameter,
isobaric heat capacity, isometric heat capacity, volume expansivity,
isoenthalpic Joule-Thomson coefficient, isothermal Joule-Thomson
coefficient, speed of sound
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Basic Trajectory Information
use animation toolbar to step through the trj file
.xtd is the trj file
sim. parameters
.xcd files for
energy, T,
density, and cell
The Trajectory
menu provide
current frame
information
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Advanced Analysis
Modules → Forcite → Analysis
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6. Continue from a previous simulation run
1. select the trajectory (xtd) that you wish to continue
2. Modules → Forcite → Calculation → Setup
3. Check “Restart” and “Append to current trajectory”
4. Run
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7. Create Animation (Making movies)
1. select the trajectory (xtd) from which the animation will be created
2. File → Export → Export type as “Movie Clip (*.avi)”
3. Click on the “option” button to specify the movie parameters
4. OK and Export
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