denbias (c46b2)
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