FUSIONPOREEXPANSIONP
 This is part of the membranefusion module It is only available if you configure PLUMED with ./configure –enable-modules=membranefusion . Furthermore, this feature is still being developed so take care when using it and report any problems on the mailing list.

A CV for inducing the expansion of a fusion pore from a nucleated fusion pore.

Calculate the collective variable designed by Hub [70] and implemented into PLUMED by Masone and collaborators. This CV is capable of inducing the expansion of the fusion pore from a nucleated fusion pore.

$\xi_e = \frac{R(r) - R_0}{R_0}$

Where $$\xi_e$$ is the CV, $$R_0$$ is a normalization constant that makes zero the initial value of $$\xi_e$$, and $$R(r)$$ is the approximate radius of the fusion pore, which is defined by the number of waters and phosphateoxygens beads within a horizontal layer in the center of both membranes.

Examples

This example induces the expansion of a nucleated fusion pore ( $$\xi_e = 0.75$$) from a just nucleated fusion pore ( $$\xi_e = 0.00$$).

Click on the labels of the actions for more information on what each action computes
lMem: GROUP =1-10752,21505-22728,23953-24420 #All the lower membrane beads.
uMem: GROUP =10753-21504,22729-23952,24421-24888 #All the upper membrane beads.
tails: GROUP =8-23948:12,12-23952:12,23966-24884:18,23970-24888:18 #All the lipid tails beads (from the lower and upper membrane).
waters: GROUP =24889-56589 #All the water beads.
po4: GROUP =2-23942:12,23957-24875:18 #All the lipid phosphateoxygens beads.
fusionPoreExpansion: FUSIONPOREEXPANSIONP =uMem =lMem =tails =waters =po4 =85 =7.0 =0.57
MOVINGRESTRAINT ...
=fusionPoreExpansion
=0 =0.0 =10000.0
=500000 =0.75 =10000.0
...
PRINT ARG=fusionPoreExpansion FILE=COLVAR STRIDE=1
Glossary of keywords and components
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