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.
This example induces the expansion of a nucleated fusion pore ( \(\xi_e = 0.75\)) from a just nucleated fusion pore ( \(\xi_e = 0.00\)).
lMem: GROUPPRINT ARG=fusionPoreExpansion FILE=COLVAR STRIDE=1ATOMS=1-10752,21505-22728,23953-24420 #All the lower membrane beads. uMem: GROUPthe numerical indexes for the set of atoms in the group.ATOMS=10753-21504,22729-23952,24421-24888 #All the upper membrane beads. tails: GROUPthe numerical indexes for the set of atoms in the group.ATOMS=8-23948:12,12-23952:12,23966-24884:18,23970-24888:18 #All the lipid tails beads (from the lower and upper membrane). waters: GROUPthe numerical indexes for the set of atoms in the group.ATOMS=24889-56589 #All the water beads. po4: GROUPthe numerical indexes for the set of atoms in the group.ATOMS=2-23942:12,23957-24875:18 #All the lipid phosphateoxygens beads. fusionPoreExpansion: FUSIONPOREEXPANSIONPthe numerical indexes for the set of atoms in the group.UMEMBRANE=uMemall the beads of the upper membrane..LMEMBRANE=lMemall the beads of the lower membrane..TAILS=tailsall the tail beads of the system..WATERS=watersall the water beads of the system..PHOSPHATEOXYGENS=po4all the lipid phosphateoxygens beads of the system..NSMEM=85compulsory keyword the number of slices of the membrane fusion cylinder.D=7.0compulsory keyword horizontal layer thickness, it depends on the Z separation of the membranes.R0=0.57 MOVINGRESTRAINT ...could not find this keywordARG=fusionPoreExpansionthe input for this action is the scalar output from one or more other actions.STEP0=0compulsory keyword This keyword appears multiple times as STEPx with x=0,1,2,...,n.AT0=0.0compulsory keyword ATx is equal to the position of the restraint at time STEPx.KAPPA0=10000.0compulsory keyword KAPPAx is equal to the value of the force constants at time STEPx.STEP1=500000compulsory keyword This keyword appears multiple times as STEPx with x=0,1,2,...,n.AT1=0.75compulsory keyword ATx is equal to the position of the restraint at time STEPx.KAPPA1=10000.0 ...compulsory keyword KAPPAx is equal to the value of the force constants at time STEPx.
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 |
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 |
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. |
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. |