Fill Cell

Description

This function fills the cell with copies of other components or systems. For more details on the algorithm, refer to the documentation for create and fill cell. In this case, the process starts with a non-empty cell.

Latest version

Allowed number of parents: 2 or 3

  1. Parent system

  2. System to insert

  3. System to insert

Parameter Description Value type Value restrictions Default value Units

Total number of components

The number of components to insert. We have one entry for each parent component (max2)

int

≥0

0

N/A

Orientation

The orientation of the components to be inserted

selector

random, regular

random

N/A

Position

The position within the cell where the components shall be inserted

selector

random, spacefilling

random

N/A

Minimum distance between atoms

Minimum distance between the atoms of the inserted component and the existing system. We have one entry for each inserted component (maximum two entries)

float

>0

2.0

Angstrom

Periodic boundary conditions

Indicates whether we have periodic boundary conditions in x, y and z

boolean

true, False

[True, True,True]

N/A

Seed for random generation

The seed used in the random generator, -1 can be selected for a random seed

int

>-1

123

N/A

Enable minimization

Indicates if a GROMACS energy minimization should be performed to increase the insertion success rate

boolean

True, False

False

N/A

Number of steps

Maximum number of steps in the energy minimization

integer

>0

5000

N/A

Convergence criterion for energy minimization

Force convergence criterion for the energy minimization

float

0 < x < 10000

100

kJ mol-1 nm-1

Initial step for energy minimization

The initial step size for the energy minimization

float

0 < x < 0.1

0.001

nm

Distance limit for energy minimization

If the minimization is enabled, it indicates the minimum distance between the inserted component and the existing system before the minimization

float

>0

0.5

Angstrom