   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  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 ATOMSthe numerical indexes for the set of atoms in the group. =1-10752,21505-22728,23953-24420 #All the lower membrane beads.
uMem: GROUP ATOMSthe numerical indexes for the set of atoms in the group. =10753-21504,22729-23952,24421-24888 #All the upper membrane beads.
tails: GROUP ATOMSthe numerical indexes for the set of atoms in the 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 ATOMSthe numerical indexes for the set of atoms in the group. =24889-56589 #All the water beads.
po4: GROUP ATOMSthe numerical indexes for the set of atoms in the group. =2-23942:12,23957-24875:18 #All the lipid phosphateoxygens beads.
fusionPoreExpansion: FUSIONPOREEXPANSIONP UMEMBRANEall the beads of the upper membrane.. =uMem LMEMBRANEall the beads of the lower membrane.. =lMem TAILSall the tail beads of the system.. =tails WATERSall the water beads of the system.. =waters PHOSPHATEOXYGENSall the lipid phosphateoxygens beads of the system.. =po4 NSMEMcompulsory keyword
the number of slices of the membrane fusion cylinder. =85 Dcompulsory keyword
horizontal layer thickness, it depends on the Z separation of the membranes. =7.0 R0 could not find this keyword =0.57
MOVINGRESTRAINT ...
ARGthe input for this action is the scalar output from one or more other actions. =fusionPoreExpansion
STEP0compulsory keyword
This keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n. =0 AT0compulsory keyword
AT\f$x\f$ is equal to the position of the restraint at time STEP\f$x\f$. =0.0 KAPPA0compulsory keyword
KAPPA\f$x\f$ is equal to the value of the force constants at time STEP\f$x\f$. =10000.0
STEP1compulsory keyword
This keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n. =500000 AT1compulsory keyword
AT\f$x\f$ is equal to the position of the restraint at time STEP\f$x\f$. =0.75 KAPPA1compulsory keyword
KAPPA\f$x\f$ is equal to the value of the force constants at time STEP\f$x\f$. =10000.0
...

PRINT ARG=fusionPoreExpansion FILE=COLVAR STRIDE=1
Glossary of keywords and components
The atoms involved can be specified using