MEMFUSIONP
 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.

Calculate a CV that can induce the formation of the hemifusion stalk between two initially flat and planar bilayers.

Calculate the collective variable designed by Hub and collaborators [69] and implemented into PLUMED by Masone and collaborators [50] . This CV is capable of inducing the formation of the hemifusion stalk between two initially flat and planar bilayers surrounded by water molecules.

$\xi_f = \frac{1}{N_{sf}} \sum_{s=0}^{N_{sf}-1} \delta_{sf} (N_{sf}^{(p)})$

Where $$\xi_f$$ is the CV, $$N_{sf}$$ is the number of slices of the cylinder that make up the CV, $$\delta_{sf}$$ 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 tail beads within the slice s.

Examples

This example induces a hemifusion stalk ( $$\xi_f = 0.85$$) from a pair of initially flat membranes ( $$\xi_f = 0.2$$).

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. =1-12288 #All the lower membrane beads.
uMem: GROUP ATOMSthe numerical indexes for the set of atoms in the group. =12289-24576 #All the upper membrane beads.
tails: GROUP ATOMSthe numerical indexes for the set of atoms in the group. =8-24572:12,12-24576:12 #All the lipid tails beads (from the lower and upper membrane).
memFusion: MEMFUSIONP UMEMBRANEall the beads of the upper membrane. =uMem LMEMBRANEall the beads of the lower membrane. =lMem TAILSall the tail beads of the system. =tails NSMEMcompulsory keyword
the number of slices of the membrane fusion cylinder in such a way that when the
bilayers are flat and parallel the CV is equal to 0.2. =70 DSMEM( default=0.1) =0.1 HMEM( default=0.25 =0.25 RCYLMEM( default=1.75 =1.75 ZETAMEM( default=0.5 =0.5
MOVINGRESTRAINT ...
ARGthe input for this action is the scalar output from one or more other actions. =memFusion
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$x\f$. =0.85 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=memFusion FILE=COLVAR STRIDE=1

You can test this CV with another example in this GitHub folder.

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
Compulsory keywords
 NSMEM the number of slices of the membrane fusion 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. RCYLMEM ( default=1.75 ) the radius of the membrane fusion cylinder. ZETAMEM ( default=0.5 ) occupation factor. ONEOVERS2C2CUTOFF ( default=500 ) cut off large values for the derivative of the atan2 function. XCYL X coordinate of the fixed cylinder, if not present this will be calculated. YCYL Y coordinate of the fixed cylinder, if not present this will be calculated.