   FUSIONPORENUCLEATIONP
 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 nucleation of the fusion pore from a hemifusion stalk.

Calculate the collective variable designed by Hub and collaborators  and implemented into PLUMED by Masone and collaborators. This CV is capable of inducing the nucleation of the fusion pore from a hemifusion stalk.

$\xi_n = \frac{1}{N_{sn}} \sum_{s=0}^{N_{sn}-1} \delta_{sn} (N_{sn}^{(p)})$

Where $$\xi_n$$ is the CV, $$N_{sn}$$ is the number of slices of the cylinder that make up the CV, $$\delta_{sn}$$ is a continuos function in the interval [0 1] ( $$\delta_{sf} = 0$$ for no beads in the slice s, and $$\delta_{sf} = 1$$ for 1 or more beads in the slice s) and $$N_{sf}^{(p)}$$ accounts for the number of water and phosphateoxygens beads within the slice s.

Examples

This example induces the nucleation of the fusion pore ( $$\xi_n = 1.0$$) from a hemifusion stalk ( $$\xi_n = 0.2$$).

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. =24889-56490 #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.
fusionPoreNucleation: FUSIONPORENUCLEATIONP 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 NScompulsory keyword
the number of slices of the membrane-spanning cylinder in such a way that when the
bilayers are flat and parallel the CV is equal to 0.2. =45
MOVINGRESTRAINT ...
ARGthe input for this action is the scalar output from one or more other actions. =fusionPoreNucleation
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$x\f$. =0.2 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$x\f$. =1.0 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=fusionPoreNucleation FILE=COLVAR STRIDE=1
Glossary of keywords and components
The atoms involved can be specified using