Lecture 7: Coarse Grain simulations Flashcards
What do reduced units allow for?
Time, mass etc to be expressed in unitless quantities
What is the law of corresponding states?
There are infinitely many combinations that all correspond to the same reduced units
Why are reduced units useful?
Avoids errors from working with very small numbers from SI units
How can reduced units be thought of?
Rescaling so that corresponding states collapse onto one line
Where do reduced length units come from?
From the LJ potential
Length unit σ
Mass unit energy unit ε
What is reduced length equation? If σ =length of argon atom
r*=r/σ
Where do reduced units of time come from?
From the LJ potential
How do we find reduced units of time?
Find a combination of length, mass and energy units that give a unit of time
Use units from LJ potential
Take a product of arbitrary powers of these contacts and equate for s^1
Why is using reduced units good for larger systems?
More Computationally efficient
What is coarse groaning?
Representing more than one atom as a single bead by grouping them together
What is least coarse graining?
United atom that represents -CH2 as one bead with no explicit hydrogens
What are some advantages of coarse graining?
-allows larger system sizes
-allows longer timescales
What are some disadvantages of coarse graining?
-lose finer detail such as hydrogen bonding
-don’t always know what is a reasonable assumption/CG scheme to capture all the underlying physics/chemistry and won’t know until comparison with experimental data
What is a bottom up approach?
Match model to quantum mechanical or atomistic simulations
-first step to decide on mapping scheme- what atoms in what beads
What is the iterative Boltzmann inversion?
-generates non-analytical potential U(r)
-iterative so repeats until threshold tolerance value met
-generally done to compare from atomistic simulations based on CG scheme
