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# denbias (c47b2)

DENBIAS Module of CHARMM

Recently developed DENBIAS (DENsity BIASing) module calculates the density of

a particular molecular species in a cylindrical volume aligned to the Z-axis.

* Syntax | Syntax of the DENBIAS command

* Function | Purpose of each of the command

* Examples | Usage examples of the DENBIAS module

Recently developed DENBIAS (DENsity BIASing) module calculates the density of

a particular molecular species in a cylindrical volume aligned to the Z-axis.

* Syntax | Syntax of the DENBIAS command

* Function | Purpose of each of the command

* Examples | Usage examples of the DENBIAS module

Top

Syntax of the DENBIAS Command

[SYNTAX DENBIAS]

DBIAs [CLEAr] [ANAL] [config-options]

config-options:

{ASEL|DSEL atom-selection-1 [atom-selection-2]}

RCYL real

RW real

ZUP real

ZLOW real

ZW real

FORC real

TDEN real

Syntax of the DENBIAS Command

[SYNTAX DENBIAS]

DBIAs [CLEAr] [ANAL] [config-options]

config-options:

{ASEL|DSEL atom-selection-1 [atom-selection-2]}

RCYL real

RW real

ZUP real

ZLOW real

ZW real

FORC real

TDEN real

Top

CLEAr Clears the memory and deallocates the arrays.

ANAL Calculates the values of number density of selected species

and their differences and reports them in units of 1/nm^3.

config-options:

atom-selection: Atom selection is invoked by CHARMM standard select command.

Selected atoms are to be considered for density biasing potential. If only

one selection is performed (ASEL), the potential function is made by:

1/2 * FORC * (density_of_selected_atoms - TDEN)^2

If double selection is performed (DSEL), the difference between the densities

of these two selections will construct the reaction coordinate for biasing

potential:

1/2 * FORC * ((density_of_selected_1 - density_of_selected_2) - TDEN)^2

Cylinder-specification:

The parameters for the cylinder, such as radius of cylinder (RCYL), the range

of cylinder height (ZLow to ZUp), and the switching distance in radial (RW)

and axial (ZW) directions are specified.

RCYL radius of cylinder (real) in Angstroms

RW width of switching region in radial direction (real) in Angstroms

ZLOW lower bound of cylinder on the Z-exis (real) in Angstroms

ZUP upper bound of cylinder on the Z-exis (real) in Angstroms

ZW width of switching region in z-direction (real) in Angstroms

Force-specification:

The parameters for the potential function is given by FORC (the force constant),

and TDEN the target equilibrium density.

FORCe force constant (real) in kcal/mol/nm^6

TDEN target density (real) in 1/nm^3

CLEAr Clears the memory and deallocates the arrays.

ANAL Calculates the values of number density of selected species

and their differences and reports them in units of 1/nm^3.

config-options:

atom-selection: Atom selection is invoked by CHARMM standard select command.

Selected atoms are to be considered for density biasing potential. If only

one selection is performed (ASEL), the potential function is made by:

1/2 * FORC * (density_of_selected_atoms - TDEN)^2

If double selection is performed (DSEL), the difference between the densities

of these two selections will construct the reaction coordinate for biasing

potential:

1/2 * FORC * ((density_of_selected_1 - density_of_selected_2) - TDEN)^2

Cylinder-specification:

The parameters for the cylinder, such as radius of cylinder (RCYL), the range

of cylinder height (ZLow to ZUp), and the switching distance in radial (RW)

and axial (ZW) directions are specified.

RCYL radius of cylinder (real) in Angstroms

RW width of switching region in radial direction (real) in Angstroms

ZLOW lower bound of cylinder on the Z-exis (real) in Angstroms

ZUP upper bound of cylinder on the Z-exis (real) in Angstroms

ZW width of switching region in z-direction (real) in Angstroms

Force-specification:

The parameters for the potential function is given by FORC (the force constant),

and TDEN the target equilibrium density.

FORCe force constant (real) in kcal/mol/nm^6

TDEN target density (real) in 1/nm^3

Top

Examples

Example (1)

For biasing the density of one species (water molecules) to reach 10 (1/nm^3)

with force constant of 10 kcal/mol/nm^6 in a cylinder with radius of 8 Angstroms

that spans from 0 to 18 Angstroms:

DBIAs ASEL select resn tip3 end RCYL 8 RW 1 ZUP 18 ZLOW 0 FORC 10 TDEN 10

Example (2)

For biasing the difference in densities of two species (HELT and HELM) to

reach 20.0 (1/nm^3) with force constant of 10 kcal/mol/nm^6 in a cylinder of

radius 50 Angstroms that spans from -inf to +inf:

DBIAs DSEL select resn helt end -

select resn helm end -

RCYL 50 RW 1 ZUP 100 ZLOW -100 FORC 10 TDEN 20.0

Example (3)

Calculating the number densities of two residues called HELM and HELT:

DBIAs DSEL select resn helt end select resn helm end rcyl 50 rw 1 zup 25 zlow -25

DBIAs ANAL

Examples

Example (1)

For biasing the density of one species (water molecules) to reach 10 (1/nm^3)

with force constant of 10 kcal/mol/nm^6 in a cylinder with radius of 8 Angstroms

that spans from 0 to 18 Angstroms:

DBIAs ASEL select resn tip3 end RCYL 8 RW 1 ZUP 18 ZLOW 0 FORC 10 TDEN 10

Example (2)

For biasing the difference in densities of two species (HELT and HELM) to

reach 20.0 (1/nm^3) with force constant of 10 kcal/mol/nm^6 in a cylinder of

radius 50 Angstroms that spans from -inf to +inf:

DBIAs DSEL select resn helt end -

select resn helm end -

RCYL 50 RW 1 ZUP 100 ZLOW -100 FORC 10 TDEN 20.0

Example (3)

Calculating the number densities of two residues called HELM and HELT:

DBIAs DSEL select resn helt end select resn helm end rcyl 50 rw 1 zup 25 zlow -25

DBIAs ANAL