Dry System

Description

This node allows to slowly remove the solvent in order to emulate a drying process. The solvent is progressively removed during a number of cycles defined by the user. After every drying cycle, one equilibration simulation is automatically performed to compress the simulation cell and avoid the appereance of artificial holes that could hamper the performance of the simulations. The compression can be tuned to be isotropic or semiisotropic (x/y). It is possible to leave a residual amount of solvent.

Latest version

Allowed number of parents: 1

  1. Simulation cell containing solvent

Parameter Description Value type Value restrictions Default value Units

Solvent name

Component name of the solvent to be removed

selector

component type

empty

N/A

Drying cycles

Number of drying cycles

integer

≥0

20

N/A

Type of residual percentage

Indicates how the residual percentage shall be calculated

selector

Initial solvent, total final weight

Initial solvent

N/A

Residual percentage

The final residual percentage of solvent that is left at the end of the drying cycles

float

≥0

0

%

Reference temperature

Indicates the reference temperature for the temperature coupling

float

≥0

300

K

Compression pressure

Pressure to compress the system after solvent removal in each drying cycle

float

>0

10

bar

Compression mode

Indicate how the simulation cell shall be compressed after each drying cycle

selector

isotropic, semiisotropic

semiisotropic

N/A

Compression duration with restraints

Indicates the duration of the compression without restraints

float

≥0

50

ps

Compression duration without restraints

Indicates the duration of the compression with restraints

float

≥0

50

ps

Time step

Time step of the compression simulation

floating

0.01 ≥ x ≥ 0

0.002

ps

Periodic boundary conditions

Indicate the periodic boundary conditions

selector

xyz, xy

xyz

N/A

Number of walls

When set to 1 there is a wall at z=0, when set to 2 there is also a wall at z=z-box

selector

0,1,2

2

N/A

Type of potential wall

9-3 (LJ 9-3 integrated over the volume behind the wall), 10-4 (LJ 10-4 integrated over the wall surface), 12-6 (direct LJ potential with the z distance from the wall)

selector

9-3, 10-4, 12-6

9-3

N/A

Wall density

Number density of the atoms for each wall

float

≥0

35

[nm-3] / [nm-2]

Atom type name in force field

Name for the wall atom type in the force field. It will be automatically inserted in the topology file for the run

string

N/A

ar

N/A

Sigma for the atom type

Sigma of the atom type, necessary to define the potential

float

N/A

-0.337

nm

Epsilon for the atom type

Epsilon of the atom type, necessary to define the potential

float

N/A

0.940

kJ/mol

Linear potential continuation beyond wall

Below this distance from wall the potential is continued linearly and thus the force is constant. Setting to a positive value is useful for equilibrations with atoms beyond wall

float

N/A

0.2

nm

Expert parameters

Parameter Description Value type Value restrictions Default value Units

Temperature coupling mode

Indicates which temperature coupling mode shall be applied

selector

v-rescale, berendsen, nose-hoover

v-rescale

N/A

Time constant for temperature coupling

Indicates the time constant for the temperature coupling

float

> 0

0.2

ps

Pressure coupling mode

Indicates which pressure coupling mode shall be applied

selector

c-rescale, berendsen, parrinello-rahman

c-rescale

N/A

Time constant for pressure coupling

Indicates the time constant for the pressure coupling

float

> 0

1.0

ps

Scaling factor for the third box vector

For Ewald summation only. Can only be used with nwall=2, where one should use ewald-geometry=3dc. The empty layer in the box serves to decrease the unphysical Coulomb interaction between periodic images

float

≥2

2

N/A

Mass of the atom type

Mass of the atom type

float

>0

39.948

atomic mass unit

Charge of the atom type

Charge of the atom type

integer

N/A

0

elementary charge