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 [70] 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
tested on v2.9
lMem: GROUP 
ATOMS
the numerical indexes for the set of atoms in the group.
=1-10752,21505-22728,23953-24420 #All the lower membrane beads. uMem: GROUP
ATOMS
the numerical indexes for the set of atoms in the group.
=10753-21504,22729-23952,24421-24888 #All the upper membrane beads. tails: GROUP
ATOMS
the 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
ATOMS
the numerical indexes for the set of atoms in the group.
=24889-56589 #All the water beads. po4: GROUP
ATOMS
the numerical indexes for the set of atoms in the group.
=2-23942:12,23957-24875:18 #All the lipid phosphateoxygens beads. fusionPoreExpansion: FUSIONPOREEXPANSIONP
UMEMBRANE
all the beads of the upper membrane..
=uMem
LMEMBRANE
all the beads of the lower membrane..
=lMem
TAILS
all the tail beads of the system..
=tails
WATERS
all the water beads of the system..
=waters
PHOSPHATEOXYGENS
all the lipid phosphateoxygens beads of the system..
=po4
NSMEM
compulsory keyword the number of slices of the membrane fusion cylinder.
=85
D
compulsory keyword horizontal layer thickness, it depends on the Z separation of the membranes.
=7.0
R0
could not find this keyword
=0.57 MOVINGRESTRAINT ...
ARG
the input for this action is the scalar output from one or more other actions.
=fusionPoreExpansion
STEP0
compulsory keyword This keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n.
=0
AT0
compulsory keyword AT\f$x\f$ is equal to the position of the restraint at time STEP\f$x\f$.
=0.0
KAPPA0
compulsory keyword KAPPA\f$x\f$ is equal to the value of the force constants at time STEP\f$x\f$.
=10000.0
STEP1
compulsory keyword This keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n.
=500000
AT1
compulsory keyword AT\f$x\f$ is equal to the position of the restraint at time STEP\f$x\f$.
=0.75
KAPPA1
compulsory 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
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.