Functions/Subroutines
program	three_bead_enzyme
	Simulate a three bead enzyme model. More...

double precision function	compute_bead_force ()

double precision function	compute_bead_energy (enzyme_idx, factor)

double precision function	fprime (x, theta_0)
	derivative of the angular harmonic arccos term More...

subroutine	select_substrate
	Select substrate molecules for binding to enzyme. More...

subroutine	bind_molecule (enzyme_idx, idx)
	Bind solvent molecule idx to enzyme. More...

subroutine	unbind_molecule (enzyme_idx, to_species)
	Bind solvent molecule idx to enzyme. More...

subroutine	add_energy_to_cell (cell_idx, energy)

subroutine	reset_enzyme_region_bit

subroutine	fix_neighbor_list (idx)
	Check all colloids' neighbor lists to possibly add solvent particle idx. More...

Function/Subroutine Documentation

◆ add_energy_to_cell()

subroutine three_bead_enzyme::add_energy_to_cell	(	integer, intent(in)	cell_idx,
		double precision, intent(in)	energy
	)

Definition at line 961 of file three_bead_enzyme.f90.

◆ bind_molecule()

subroutine three_bead_enzyme::bind_molecule	(	integer, intent(in)	enzyme_idx,
		integer, intent(in)	idx
	)

Bind solvent molecule idx to enzyme.

Definition at line 842 of file three_bead_enzyme.f90.

◆ compute_bead_energy()

double precision function three_bead_enzyme::compute_bead_energy	(	integer, intent(in)	enzyme_idx,
		integer, intent(in)	factor
	)

Definition at line 706 of file three_bead_enzyme.f90.

◆ compute_bead_force()

double precision function three_bead_enzyme::compute_bead_force ( )

Definition at line 670 of file three_bead_enzyme.f90.

◆ fix_neighbor_list()

subroutine three_bead_enzyme::fix_neighbor_list ( integer, intent(in) idx )

Check all colloids' neighbor lists to possibly add solvent particle idx.

Definition at line 1068 of file three_bead_enzyme.f90.

◆ fprime()

double precision function three_bead_enzyme::fprime	(	double precision, intent(in)	x,
		double precision, intent(in)	theta_0
	)

derivative of the angular harmonic arccos term

Definition at line 731 of file three_bead_enzyme.f90.

◆ reset_enzyme_region_bit()

subroutine three_bead_enzyme::reset_enzyme_region_bit ( )

Definition at line 1042 of file three_bead_enzyme.f90.

◆ select_substrate()

subroutine three_bead_enzyme::select_substrate ( )

Select substrate molecules for binding to enzyme.

All substrate molecules are tested for their distance to the enzyme active site and are allowed to react once per stay in the enzyme region.

Definition at line 745 of file three_bead_enzyme.f90.

◆ three_bead_enzyme()

program three_bead_enzyme ( )

Simulate a three bead enzyme model.

Parameters

L	length of simulation box in the 3 dimensions
rho	fluid number density
T	Temperature. Used for setting initial velocities and (if enabled) bulk thermostatting.
tau	MPCD collision time
N_enzymes	Number of enzyme molecules
substrate_fraction	initial fraction of non-inert (substrate and product) fluid particles
product_relative_fraction	inital relative fraction of product among non-inert fluid particles
N_MD	number MD steps occuring in tau
N_loop	number of MPCD timesteps
colloid_sampling	interval (in MD steps) of sampling the colloid position and velocity
equilibration_loops	number of MPCD steps for equilibration
sigma_E	radius of enzymatic_site
sigma_N	radius of N sphere
link_d	length of rigid link
link_angles	angle of the model at rest
elastic_k	stiffness of the link
angle_k	stiffness of the angular link
epsilon_E	interaction parameter of E sphere with solvent species (3 elements)
epsilon_N	interaction parameter of N sphere with solvent species (3 elements)
epsilon_colloid	interaction parameter among colloids
enzyme_capture_radius	capture and release radius for substrate/product
rate_release_s	rate of release of substrate from enzyme
rate_release_p	rate of release of product from enzyme
proba_s	probability of capture of substrate
proba_p	probability of capture of product
bulk_rmpcd	use bulkd rmpcd reaction for B->A instead of resetting
immediate_chemistry	start to process chemical event before sampling
bulk_rate	rates for the A->B and B->A bulk reaction

Definition at line 36 of file three_bead_enzyme.f90.

◆ unbind_molecule()

subroutine three_bead_enzyme::unbind_molecule	(	integer, intent(in)	enzyme_idx,
		integer, intent(in)	to_species
	)