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

PRINT ARG=memFusion FILE=COLVAR STRIDE=1lMem:GROUPATOMS=1-12288 #All the lower membrane beads.the numerical indexes for the set of atoms in the group.uMem:GROUPATOMS=12289-24576 #All the upper membrane beads.the numerical indexes for the set of atoms in the group.tails:GROUPATOMS=8-24572:12,12-24576:12 #All the lipid tails beads (from the lower and upper membrane).the numerical indexes for the set of atoms in the group.memFusion:MEMFUSIONPUMEMBRANE=all the beads of the upper membrane.uMemLMEMBRANE=all the beads of the lower membrane.lMemTAILS=all the tail beads of the system.tailsNSMEM=70compulsory keywordthe 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.DSMEM=0.1( default=0.1)HMEM=0.25( default=0.25RCYLMEM=1.75( default=1.75ZETAMEM=0.5 MOVINGRESTRAINT ...( default=0.5ARG=the input for this action is the scalar output from one or more other actions.memFusionSTEP0=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=0.85compulsory 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$x\f$.

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. |