Anion transporters research using MD simulations.

Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate


Docking and homology modeling explain inhibition of the human vesicular glutamate transporters

molecular dynamics results analysis

Good explanation of Essential Dynamics: PDF.

Steered MD again

guys compared different pulling rates

Steered MD in GROMACS (pull code)

The pull code allows to apply a force between two centers of mass (for >1 groups). It appears to be useful to simulate protein penetration into lipid membrane (channel formation). Config must have a following lines:
pull_start = yes
pull_init1 = 0
pull = umbrella
pull_geometry = direction
pull_group0 = Protein
pull_group1 = POPC
pull_vec1 = 0 0 0.5
pull_k1 = 3000
pull_rate1 = 0.01 ; nm/ps Extreme parameters for extreme pulling

discussions: [1], [2]

b-Amyloid Ion Channels

Models of b-Amyloid Ion Channels in the Membrane Suggest That Channel Formation in the Bilayer Is a Dynamic Process: amyloid ion channel formation mechanism suggested (src)