Action: FUSIONPOREEXPANSIONP
| Module | membranefusion |
|---|---|
| Description | Usage |
| A CV for inducing the expansion of a fusion pore from a nucleated fusion pore. |   |
| 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 |
| D | compulsory | none | horizontal layer thickness, it depends on the Z separation of the membranes |
| R0 | compulsory | none | normalization constant that makes 0 the initial value of the CV |
| 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 |
| VO | optional | not used | beads’ molecular volume |
| H | optional | not used | parameter of the step function θ(x,h) for the fusion pore expansion |
| RMAX | optional | not used | to avoid effects of membrane undulations in large membranes (more than 256 lipids) |
| 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 |