RMPCDMD
Functions/Subroutines
three_bead_enzyme.f90 File Reference

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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
Llength of simulation box in the 3 dimensions
rhofluid number density
TTemperature. Used for setting initial velocities and (if enabled) bulk thermostatting.
tauMPCD collision time
N_enzymesNumber of enzyme molecules
substrate_fractioninitial fraction of non-inert (substrate and product) fluid particles
product_relative_fractioninital relative fraction of product among non-inert fluid particles
N_MDnumber MD steps occuring in tau
N_loopnumber of MPCD timesteps
colloid_samplinginterval (in MD steps) of sampling the colloid position and velocity
equilibration_loopsnumber of MPCD steps for equilibration
sigma_Eradius of enzymatic_site
sigma_Nradius of N sphere
link_dlength of rigid link
link_anglesangle of the model at rest
elastic_kstiffness of the link
angle_kstiffness of the angular link
epsilon_Einteraction parameter of E sphere with solvent species (3 elements)
epsilon_Ninteraction parameter of N sphere with solvent species (3 elements)
epsilon_colloidinteraction parameter among colloids
enzyme_capture_radiuscapture and release radius for substrate/product
rate_release_srate of release of substrate from enzyme
rate_release_prate of release of product from enzyme
proba_sprobability of capture of substrate
proba_pprobability of capture of product
bulk_rmpcduse bulkd rmpcd reaction for B->A instead of resetting
immediate_chemistrystart to process chemical event before sampling
bulk_raterates 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 
)

Bind solvent molecule idx to enzyme.

Definition at line 900 of file three_bead_enzyme.f90.