Action: FUSIONPORENUCLEATIONP

Module	membranefusion
Description	Usage
A CV for inducing the nucleation of the fusion pore from a hemifusion stalk.
output value	type
the value of the CV	scalar

Details and examples

A CV for inducing the nucleation of the fusion pore from a hemifusion stalk.

Calculate the collective variable designed by Hub and collaborators (see paper below) and implemented into PLUMED by Masone and collaborators. This CV is capable of inducing the nucleation of the fusion pore from a hemifusion stalk.

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

Where $\xi_n$ is the CV, $N_{sn}$ is the number of slices of the cylinder that make up the CV, $\delta_{sn}$ 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 water and phosphateoxygens beads within the slice s.

Examples

This example induces the nucleation of the fusion pore ($\xi_n = 1.0$) from a hemifusion stalk ($\xi_n = 0.2$).

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=1-10752,21505-22728,23953-24420 #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=10753-21504,22729-23952,24421-24888 #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=8-23948:12,12-23952:12,23966-24884:18,23970-24888:18 #All the lipid tails beads (from the lower and upper membrane).
watersThe GROUP action with label waters calculates the following quantities:
 Quantity   
 Type   
 Description  
waters
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=24889-56490 #All the water beads.
po4The GROUP action with label po4 calculates the following quantities:
 Quantity   
 Type   
 Description  
po4
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=2-23942:12,23957-24875:18 #All the lipid phosphateoxygens beads.

fusionPoreNucleationThe FUSIONPORENUCLEATIONP action with label fusionPoreNucleation calculates the following quantities:
 Quantity   
 Type   
 Description  
fusionPoreNucleation
scalar
the value of the CV: FUSIONPORENUCLEATIONPA CV for inducing the nucleation of the fusion pore from a hemifusion stalk. 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 WATERSall the water beads of the system=waters PHOSPHATEOXYGENSall the lipid phosphateoxygens beads of the system=po4 NSMEMthe number of slices of the membrane fusion cylinder=85 NSthe number of slices of the membrane-spanning cylinder in such a way that when the bilayers are flat and parallel the CV is equal to 0=45

MOVINGRESTRAINTAdd a time-dependent, harmonic restraint on one or more variables. More details ...
    ARGthe labels of the scalars on which the bias will act=fusionPoreNucleation
    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=1.0 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=fusionPoreNucleation 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

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
WATERS	atoms	all the water beads of the system
PHOSPHATEOXYGENS	atoms	all the lipid phosphateoxygens 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
WATERS	input	none	all the water beads of the system
PHOSPHATEOXYGENS	input	none	all the lipid phosphateoxygens beads of the system
NSMEM	compulsory	none	the number of slices of the membrane fusion cylinder
NS	compulsory	none	the number of slices of the membrane-spanning 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
DSMEMThis keyword do not have examples	optional	not used	thickness of the slices of the membrane fusion cylinder
HMEMThis keyword do not have examples	optional	not used	parameter of the step function θ(x,h) for the membrane fusion
DSThis keyword do not have examples	optional	not used	thickness of the slices of the membrane-spanning cylinder
HCHThis keyword do not have examples	optional	not used	parameter of the step function θ(x,h) for the CV
RCYLThis keyword do not have examples	optional	not used	the radius of the membrane-spanning cylinder
ZETAThis keyword do not have examples	optional	not used	parameter of the switch function ψ(x,ζ)
ONEOVERS2C2CUTOFFThis keyword do not have examples	optional	not used	cut off large values for the derivative of the atan2 function to avoid violate energy
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	X 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:

• J. S. Hub, N. Awasthi, Probing a Continuous Polar Defect: A Reaction Coordinate for Pore Formation in Lipid Membranes. Journal of Chemical Theory and Computation. 13, 2352–2366 (2017)