FUSIONPOREEXPANSIONP

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 [70] 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.

- Examples

This example induces the expansion of a nucleated fusion pore ( \(\xi_e = 0.75\)) from a just nucleated fusion pore ( \(\xi_e = 0.00\)).

Click on the labels of the actions for more information on what each action computes

PRINT ARG=fusionPoreExpansion 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=24889-56589 #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.fusionPoreExpansion:FUSIONPOREEXPANSIONPUMEMBRANE=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.D=7.0compulsory keywordhorizontal layer thickness, it depends on the Z separation of the membranes.R0=0.57 MOVINGRESTRAINT ...could not find this keywordARG=the input for this action is the scalar output from one or more other actions.fusionPoreExpansionSTEP0=0compulsory keywordThis keyword appears multiple times as STEP\f$x\f$ with x=0,1,2,...,n.AT0=0.0compulsory 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=0.75compulsory 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. |

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. |

- 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. |

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. |