	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 [55] 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. 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. =24889-56589 #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
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 The FUSIONPOREEXPANSIONP action with label fusionPoreExpansion calculates a single scalar value
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 STEPx with x=0,1,2,...,n. =0 AT0compulsory keyword 
ATx is equal to the position of the restraint at time STEPx. =0.0 KAPPA0compulsory keyword 
KAPPAx is equal to the value of the force constants at time STEPx. =10000.0 
   STEP1compulsory keyword 
This keyword appears multiple times as STEPx with x=0,1,2,...,n. =500000 AT1compulsory keyword 
ATx is equal to the position of the restraint at time STEPx. =0.75 KAPPA1compulsory keyword 
KAPPAx is equal to the value of the force constants at time STEPx. =10000.0 
...The MOVINGRESTRAINT action with label 
PRINT ARGthe input for this action is the scalar output from one or more other actions. =fusionPoreExpansion FILEthe name of the file on which to output these quantities =COLVAR STRIDEcompulsory keyword ( default=1 )
the frequency with which the quantities of interest should be output =1 The PRINT action with label

Glossary of keywords and components

Description of components

By default the value of the calculated quantity can be referenced elsewhere in the input file by using the label of the action. Alternatively this Action can be used to calculate the following quantities by employing the keywords listed below. These quantities can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the quantity required from the list below.

Quantity	Description
.#!value	the value of the CV

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.
D	horizontal layer thickness, it depends on the Z separation of the membranes.
R0	normalization constant that makes 0 the initial value of the CV.

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.
VO	( default=0.076879 ) beads' molecular volume.
H	( default=0.1 ) parameter of the step function θ(x,h) for the fusion pore expansion.
RMAX	( default=2.5 ) to avoid effects of membrane undulations in large membranes (more than 256 lipids).
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.