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 |
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 |
Further details and examples
Text from manual goes here
Syntax
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_DERIVATIVES | optional | false | calculate the derivatives for these quantities numerically |
| NOPBC | 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 |
| DS | optional | not used | thickness of the slices of the membrane-spanning cylinder |
| HCH | optional | not used | parameter of the step function θ(x,h) for the CV |
| RCYL | optional | not used | the radius of the membrane-spanning cylinder |
| ZETA | optional | not used | parameter of the switch function ψ(x,ζ) |
| ONEOVERS2C2CUTOFF | optional | not used | cut off large values for the derivative of the atan2 function to avoid violate energy |
| XCYL | optional | not used | X coordinate of the fixed cylinder, if not present this will be calculated |
| YCYL | optional | not used | X coordinate of the fixed cylinder, if not present this will be calculated |