Action: MEMFUSIONP

Module	membranefusion
Description	Usage
Calculate a CV that can induce the formation of the hemifusion stalk between two initially flat and planar bilayers.
output value	type
the value of the CV	scalar

Details and examples

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 (see first paper cited below) and implemented into PLUMED by Masone and collaborators (see second paper cited below). 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

lMemThe GROUP action with label lMem calculates the following quantities: Quantity    Type    Description  
lMem atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=1-12288 #All the lower membrane beads.
uMemThe GROUP action with label uMem calculates the following quantities: Quantity    Type    Description  
uMem atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details ATOMSthe numerical indexes for the set of atoms in the group=12289-24576 #All the upper membrane beads.
tailsThe GROUP action with label tails calculates the following quantities: Quantity    Type    Description  
tails atoms indices of atoms specified in GROUP: GROUPDefine a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details 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).

memFusionThe MEMFUSIONP action with label memFusion calculates the following quantities: Quantity    Type    Description  
memFusion scalar the value of the CV: MEMFUSIONPCalculate a CV that can induce the formation of the hemifusion stalk between two initially flat and planar bilayers. More details UMEMBRANEall the beads of the upper membrane=uMem LMEMBRANEall the beads of the lower membrane=lMem TAILSall the tail beads of the system=tails NSMEMthe 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=70 DSMEM thickness of the slices of the membrane fusion cylinder=0.1 HMEM parameter of the step function θ(x,h) for the membrane fusion=0.25 RCYLMEM the radius of the membrane fusion cylinder=1.75 ZETAMEM occupation factor=0.5

MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. More details ...
    ARGthe labels of the scalars on which the bias will act=memFusion
    STEP0This keyword appears multiple times as STEPx with x=0,1,2,=0 AT0ATx is equal to the position of the restraint at time STEPx=0.2 KAPPA0KAPPAx is equal to the value of the force constants at time STEPx=10000.0
    STEP1This keyword appears multiple times as STEPx with x=0,1,2,=500000 AT1ATx is equal to the position of the restraint at time STEPx=0.85 KAPPA1KAPPAx is equal to the value of the force constants at time STEPx=10000.0
...

The MOVINGRESTRAINT action with label  calculates the following quantities: Quantity    Description  
.bias the instantaneous value of the bias potential
.work the total work performed changing this restraint
.force2 the instantaneous value of the squared force due to this bias potential
._cntr one or multiple instances of this quantity can be referenced elsewhere in the input file
._work one or multiple instances of this quantity can be referenced elsewhere in the input file
._kappa one or multiple instances of this quantity can be referenced elsewhere in the input filePRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=memFusion FILEthe name of the file on which to output these quantities=COLVAR STRIDE the frequency with which the quantities of interest should be output=1

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

Input

The atoms that serve as the input for this action are specified using one or more of the keywords in the following table.

Keyword	Type	Description
UMEMBRANE	atoms	all the beads of the upper membrane
LMEMBRANE	atoms	all the beads of the lower membrane
TAILS	atoms	all the tail beads of the system

Full list of keywords

The following table describes the keywords and options that can be used with this action

Keyword	Type	Default	Description
UMEMBRANE	input	none	all the beads of the upper membrane
LMEMBRANE	input	none	all the beads of the lower membrane
TAILS	input	none	all the tail beads of the system
NSMEM	compulsory	none	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
NUMERICAL_DERIVATIVESThis keyword do not have examples	optional	false	calculate the derivatives for these quantities numerically
NOPBCThis keyword do not have examples	optional	false	ignore the periodic boundary conditions when calculating distances
DSMEM	optional	not used	thickness of the slices of the membrane fusion cylinder
HMEM	optional	not used	parameter of the step function θ(x,h) for the membrane fusion
RCYLMEM	optional	not used	the radius of the membrane fusion cylinder
ZETAMEM	optional	not used	occupation factor
ONEOVERS2C2CUTOFFThis keyword do not have examples	optional	not used	cut off large values for the derivative of the atan2 function
XCYLThis keyword do not have examples	optional	not used	X coordinate of the fixed cylinder, if not present this will be calculated
YCYLThis keyword do not have examples	optional	not used	Y coordinate of the fixed cylinder, if not present this will be calculated

References

More information about how this action can be used is available in the following articles:

Quantity	Type	Description
lMem	atoms	indices of atoms specified in GROUP

Quantity	Description
.bias	the instantaneous value of the bias potential
.work	the total work performed changing this restraint
.force2	the instantaneous value of the squared force due to this bias potential
._cntr	one or multiple instances of this quantity can be referenced elsewhere in the input file
._work	one or multiple instances of this quantity can be referenced elsewhere in the input file
._kappa	one or multiple instances of this quantity can be referenced elsewhere in the input file