	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. The GROUP action with label lMem defines a group of atoms so that they can be referred to later in the input
uMem: GROUP ATOMSthe numerical indexes for the set of atoms in the group. =10753-21504,22729-23952,24421-24888 #All the upper membrane beads. The GROUP action with label uMem defines a group of atoms so that they can be referred to later in the input
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). The GROUP action with label tails defines a group of atoms so that they can be referred to later in the input
waters: GROUP ATOMSthe numerical indexes for the set of atoms in the group. =24889-56490 #All the water beads. The GROUP action with label waters defines a group of atoms so that they can be referred to later in the input
po4: GROUP ATOMSthe numerical indexes for the set of atoms in the group. =2-23942:12,23957-24875:18 #All the lipid phosphateoxygens beads. The GROUP action with label po4 defines a group of atoms so that they can be referred to later in the input
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 The FUSIONPORENUCLEATIONP action with label fusionPoreNucleation calculates a single scalar value
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 
...The MOVINGRESTRAINT action with label

PRINT ARG=fusionPoreNucleation FILE=COLVAR STRIDE=1

Glossary of keywords and components

The atoms involved can be specified using

UMEMBRANE	all the beads of the upper membrane.. For more information on how to specify lists of atoms see Groups and Virtual Atoms
LMEMBRANE	all the beads of the lower membrane.. For more information on how to specify lists of atoms see Groups and Virtual Atoms
TAILS	all the tail beads of the system.. For more information on how to specify lists of atoms see Groups and Virtual Atoms
WATERS	all the water beads of the system.. For more information on how to specify lists of atoms see Groups and Virtual Atoms
PHOSPHATEOXYGENS	all the lipid phosphateoxygens beads of the system.. For more information on how to specify lists of atoms see Groups and Virtual Atoms

Compulsory keywords

NSMEM	the number of slices of the membrane fusion cylinder.
NS	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.

Options

NUMERICAL_DERIVATIVES	( default=off ) calculate the derivatives for these quantities numerically
NOPBC	( default=off ) ignore the periodic boundary conditions when calculating distances
DSMEM	( default=0.1 ) thickness of the slices of the membrane fusion cylinder.
HMEM	( default=0.25 ) parameter of the step function θ(x,h) for the membrane fusion.
DS	( default=0.25 ) thickness of the slices of the membrane-spanning cylinder.
HCH	( default=0.25 ) parameter of the step function θ(x,h) for the CV.
RCYL	( default=0.8 ) the radius of the membrane-spanning cylinder.
ZETA	( default=0.75 ) parameter of the switch function ψ(x,ζ).
ONEOVERS2C2CUTOFF	( default=500 ) cut off large values for the derivative of the atan2 function to avoid violate energy.
XCYL	X coordinate of the fixed cylinder, if not present this will be calculated.
YCYL	X coordinate of the fixed cylinder, if not present this will be calculated.