FUSIONPORENUCLEATIONP

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 nucleation of the fusion pore from a hemifusion stalk.

Calculate the collective variable designed by Hub and collaborators [69] 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

PRINT ARG=fusionPoreNucleation FILE=COLVAR STRIDE=1lMem:GROUPATOMS=1-10752,21505-22728,23953-24420 #All the lower membrane beads.the numerical indexes for the set of atoms in the group.uMem:GROUPATOMS=10753-21504,22729-23952,24421-24888 #All the upper membrane beads.the numerical indexes for the set of atoms in the group.tails:GROUPATOMS=8-23948:12,12-23952:12,23966-24884:18,23970-24888:18 #All the lipid tails beads (from the lower and upper membrane).the numerical indexes for the set of atoms in the group.waters:GROUPATOMS=24889-56490 #All the water beads.the numerical indexes for the set of atoms in the group.po4:GROUPATOMS=2-23942:12,23957-24875:18 #All the lipid phosphateoxygens beads.the numerical indexes for the set of atoms in the group.fusionPoreNucleation:FUSIONPORENUCLEATIONPUMEMBRANE=all the beads of the upper membrane..uMemLMEMBRANE=all the beads of the lower membrane..lMemTAILS=all the tail beads of the system..tailsWATERS=all the water beads of the system..watersPHOSPHATEOXYGENS=all the lipid phosphateoxygens beads of the system..po4NSMEM=85compulsory keywordthe number of slices of the membrane fusion cylinder.NS=45 MOVINGRESTRAINT ...compulsory keywordthe 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 0.2.ARG=the input for this action is the scalar output from one or more other actions.fusionPoreNucleationSTEP0=0compulsory keywordThis keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n.AT0=0.2compulsory keywordAT\f$x\f$ is equal to the position of the restraint at time STEP\f$x\f$.KAPPA0=10000.0compulsory keywordKAPPA\f$x\f$ is equal to the value of the force constants at time STEP\f$x\f$.STEP1=500000compulsory keywordThis keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n.AT1=1.0compulsory keywordAT\f$x\f$ is equal to the position of the restraint at time STEP\f$x\f$.KAPPA1=10000.0 ...compulsory keywordKAPPA\f$x\f$ is equal to the value of the force constants at time STEP\f$x\f$.

- 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. |

NS | 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 0.2. |

- 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. |

DS | ( default=0.25 ) thickness of the slices of the membrane-spanning cylinder. |

HCH | ( default=0.25 ) parameter of the step function θ(x,h) for the CV. |

RCYL | ( default=0.8 ) the radius of the membrane-spanning cylinder. |

ZETA | ( default=0.75 ) parameter of the switch function ψ(x,ζ). |

ONEOVERS2C2CUTOFF | ( default=500 ) cut off large values for the derivative of the atan2 function to avoid violate energy. |

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. |