Table of Contents
MOLECULAR DYNAMICS
A. BASIS OF FORCE FIELD DRIVEN MOLECULAR DYNAMICS:
calculating new position
integration problem
delta t must be very small
General comments
The accuracy of the trajectory
Improvements...
1) Leap-frog (Verlet, 1967) Integration
PAC Integration (Harrison, 1993)
2) Non-bonded cutoff
3) Infrequent list updates (for non-bondeds)
4) The SHAKE Algorithm (van Gunsteren & Berendsen, 1977)
Improvements for accuracy. 1)Smoothing
for examples
2) Solvation
Choices, choices, choices…
B. Getting Started.
Applying the velocities
2) EQUILIBRATION
C. Different Types of MD Runs
nVE = constant
nVT = constant (two approaches)
the current temperature
nPH = constant
References
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Author:
John E. Wampler
Email:
wampler@bchiris.bmb.uga.edu
Home Page:
http://selene.biochem.uga.edu
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M.D. References
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