GRIFFIN
implicit force grid


2021

René Staritzbichler

GRIFFIN

Molecular dynamics

  • point like atoms
  • Newtons equation of motion
  • highly accurate, yet very time-consuming
    • small timesteps
    • large number of pair interactions
  • cannot resolve clashes in starting conformation

Speed MD up


Overcoming time and size limitations by simplification

  • molecule: coarse grained simulations
  • environment: implicit waters

Implicit water

  • no water molecules actually present during simulation
  • instead describe statistical effect
    • potential of mean force
    • exposure

Griffin

Implicit (potential) protein force field

  • precalculated
  • forces caused by protein are stored on grid
  • atomic detail
  • very fast
  • simplification: static protein

Potential forces

\[ \vec{F} = q_{dummy} \cdot \sum_{i=1}^{atoms} \frac{1}{4\pi \epsilon_0} \frac{q_i}{r_{i,dummy}^2} \frac{\vec{r}}{r} \]

Force grid

\[ \vec{P} = \sum_{i=1}^{atoms} \frac{1}{4\pi \epsilon_0} \frac{q_i}{r_{i,gridpoint}^2} \frac{\vec{r}}{r} \]

Forces

\[ \vec{P} = \sum_{i=1}^{atoms} \frac{1}{4\pi \epsilon_0} \frac{q_i}{r_{i,gridpoint}^2} \frac{\vec{r}}{r} \]

Resulting forces

Running MD & Griffin

MD with a ghost force field

(-: In action :-)

More action

Photosystem

Cheers!