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]
Thursday, December 17, 2009
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