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 [69] 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