SDA (SDA flex)  7.2
Simulation of Diffusional Association
Public Attributes | List of all members
mod_input_parameter::param_list Type Reference

Regroup all input parameter Used only for reading sda_input file and preparation stage, not anymore in the code after. More...

Collaboration diagram for mod_input_parameter::param_list:

Public Attributes

character(128) computation
 assign to the type type_computation: association/dissociation rate or docking or electron transfert More...
 
real(kind=8) dseed
 Variables not associated to a group. More...
 
real(kind=8) timemax
 
integer nrun
 
integer novers
 
integer napt1
 
integer napt2
 
integer nrec
 
integer save_exclusion
 
real(kind=4) probep
 
real(kind=4) probew
 
real(kind=4) hexcl
 
real(kind=4) thresold
 
real(kind=4) rboost
 
logical save_access
 
logical account_occurency
 
integer desolv_img_chg
 
real(kind=8) epsilon_scale
 
logical ignore_exclusion
 
logical record_startpos
 
logical oneway_surf_chg
 
logical old_rotation
 
type(type_calculationt_calc
 For group type calculation. More...
 
integer total_solutes
 
integer total_grids
 
real(kind=4) win0
 For rate claculation. More...
 
real(kind=4) dwin
 
integer nwin
 
integer nb_contact
 
logical ibootstrap
 
logical ifpt
 
logical stop_traj
 
logical anal_corr
 
real(kind=8) rmsd_min
 For complexes and trajectories. More...
 
integer ncmx
 
integer ntraj_rec
 
integer max_array_traj
 
integer freq_print
 
integer mem_traj_frames
 
logical ionerun
 
character(128) fcomplexes
 
character(128) ftrajectories
 
logical format_ascii_complexe
 
logical format_ascii_trajectory
 
logical traj_sum_nrj
 
logical compl_sum_nrj
 
logical rst_complex
 
integer merge_step
 
integer size_thread
 
character(128) rxna12f
 For reaction criteria. More...
 
character(128) et1f
 
character(128) et2f
 
real(kind=4) dind
 
integer nnnons
 
integer nwrec
 
integer sdamd
 
logical itimestep
 For timestep. More...
 
logical height_dependent_dt
 
real(kind=8) dt1
 
real(kind=8) swd1
 
real(kind=8) dt2
 
real(kind=8) swd2
 
real(kind=4) c
 For geometry. More...
 
real(kind=4) xmin
 
real(kind=4) xmax
 
real(kind=4) ymin
 
real(kind=4) ymax
 
real(kind=4) zmin
 
real(kind=4) zmax
 
real(kind=4) start_pos
 
real(kind=4) min_height
 
logical escape
 
logical pbc
 
logical surf_geom
 
logical half_sphere
 
integer type_geom
 
real(kind=8) epfct
 global parameter, apply to all solutes More...
 
real(kind=8) edfct
 
real(kind=8) hdfct
 
real(kind=8) ljrepfct
 
real(kind=8) ljfct
 
real(kind=8) epfct_oneway_surf
 
real(kind=4) ionic
 analytic group, only HI and DH now, crowder later More...
 
real(kind=4) h_analytic
 
real(kind=4) lvol_rcut
 
real(kind=4) surface_height
 
real(kind=4) surface_prefct
 
logical ianalytic
 
logical debyeh
 
logical hydro
 
logical dh_imgchg
 
logical dh_only
 
logical ihom_charged_surf
 
logical gouy_chapman
 
logical no_normal_hi
 
logical no_image_hi
 
logical no_height_hi
 
logical ionic_read
 
character(128) pdb_filename
 For solute group. More...
 
character(128) qef
 
character(128) epf
 
character(128) edf
 
character(128) hdf
 
character(128) lj_repf
 
character(128), dimension(:), allocatable ljf
 
character(2), dimension(:), allocatable atom_type_lj
 
real(kind=8) dm
 
real(kind=8) dr
 
real(kind=8) real_net_charge
 
real(kind=8) surface_charge_dens
 
real(kind=8) dh_rad
 
real(kind=8) rep_rad
 
real(kind=8) vol_rad
 
integer nb_solute
 
integer nb_lenjones
 
logical irot
 
logical isurf
 
logical iflex
 
logical iimg_chg
 
logical vert_excl
 
logical charge_read
 
logical radius_read
 
real(kind=8) xcent
 
real(kind=8) ycent
 
real(kind=8) zcent
 
integer total_conf
 For flexibility. More...
 
integer initial_conf
 
logical nearest_ngb
 
real(kind=4) frequence
 
real(kind=4) std_freq
 
character(128) list_conf_name
 
character(128) flex_method
 
character(128) restart_filename
 For restart. More...
 
logical irestart
 
integer fixe_bin_size
 For residence_time. More...
 
character(128) enum_str_residtime
 
real(kind=4) size_cell_x
 
real(kind=4) size_cell_y
 
real(kind=4) size_cell_z
 
real(kind=4) shift_rt_x
 
real(kind=4) shift_rt_y
 
real(kind=4) shift_rt_z
 
integer nb_cell_x
 
integer nb_cell_y
 
integer nb_cell_z
 
integer format_rt3d
 
logical pair_proteins
 
logical imetaldesolv
 Special group for MetalDesolvation, distance_to_surface, energy_per_water, radius_patch, radius_water. More...
 
real(kind=4) zadw
 
real(kind=4) eadw
 
real(kind=4) radw
 
real(kind=4) aadw
 
logical ipmf
 Group for PMF calculations. More...
 
integer mentth
 
integer mentfi
 
integer mentom
 
integer mentx
 
integer menty
 
real(kind=8) pstart
 
real(kind=8) pfinish
 
real(kind=8) dz
 

Detailed Description

Regroup all input parameter Used only for reading sda_input file and preparation stage, not anymore in the code after.

Member Data Documentation

◆ aadw

real(kind=4) mod_input_parameter::param_list::aadw

◆ account_occurency

logical mod_input_parameter::param_list::account_occurency

◆ anal_corr

logical mod_input_parameter::param_list::anal_corr

◆ atom_type_lj

character ( 2 ), dimension(:), allocatable mod_input_parameter::param_list::atom_type_lj

◆ c

real ( kind=4 ) mod_input_parameter::param_list::c

For geometry.

◆ charge_read

logical mod_input_parameter::param_list::charge_read

◆ compl_sum_nrj

logical mod_input_parameter::param_list::compl_sum_nrj

◆ computation

character ( 128 ) mod_input_parameter::param_list::computation

assign to the type type_computation: association/dissociation rate or docking or electron transfert

◆ debyeh

logical mod_input_parameter::param_list::debyeh

◆ desolv_img_chg

integer mod_input_parameter::param_list::desolv_img_chg

◆ dh_imgchg

logical mod_input_parameter::param_list::dh_imgchg

◆ dh_only

logical mod_input_parameter::param_list::dh_only

◆ dh_rad

real ( kind=8 ) mod_input_parameter::param_list::dh_rad

◆ dind

real ( kind=4 ) mod_input_parameter::param_list::dind

◆ dm

real ( kind=8 ) mod_input_parameter::param_list::dm

◆ dr

real ( kind=8 ) mod_input_parameter::param_list::dr

◆ dseed

real ( kind=8 ) mod_input_parameter::param_list::dseed

Variables not associated to a group.

◆ dt1

real ( kind=8 ) mod_input_parameter::param_list::dt1

◆ dt2

real ( kind=8 ) mod_input_parameter::param_list::dt2

◆ dwin

real ( kind=4 ) mod_input_parameter::param_list::dwin

◆ dz

real(kind=8) mod_input_parameter::param_list::dz

◆ eadw

real(kind=4) mod_input_parameter::param_list::eadw

◆ edf

character ( 128 ) mod_input_parameter::param_list::edf

◆ edfct

real ( kind=8 ) mod_input_parameter::param_list::edfct

◆ enum_str_residtime

character ( 128 ) mod_input_parameter::param_list::enum_str_residtime

◆ epf

character ( 128 ) mod_input_parameter::param_list::epf

◆ epfct

real ( kind=8 ) mod_input_parameter::param_list::epfct

global parameter, apply to all solutes

◆ epfct_oneway_surf

real ( kind=8 ) mod_input_parameter::param_list::epfct_oneway_surf

◆ epsilon_scale

real ( kind=8 ) mod_input_parameter::param_list::epsilon_scale

◆ escape

logical mod_input_parameter::param_list::escape

◆ et1f

character ( 128 ) mod_input_parameter::param_list::et1f

◆ et2f

character ( 128 ) mod_input_parameter::param_list::et2f

◆ fcomplexes

character ( 128 ) mod_input_parameter::param_list::fcomplexes

◆ fixe_bin_size

integer mod_input_parameter::param_list::fixe_bin_size

For residence_time.

◆ flex_method

character ( 128 ) mod_input_parameter::param_list::flex_method

◆ format_ascii_complexe

logical mod_input_parameter::param_list::format_ascii_complexe

◆ format_ascii_trajectory

logical mod_input_parameter::param_list::format_ascii_trajectory

◆ format_rt3d

integer mod_input_parameter::param_list::format_rt3d

◆ freq_print

integer mod_input_parameter::param_list::freq_print

◆ frequence

real ( kind=4 ) mod_input_parameter::param_list::frequence

◆ ftrajectories

character ( 128 ) mod_input_parameter::param_list::ftrajectories

◆ gouy_chapman

logical mod_input_parameter::param_list::gouy_chapman

◆ h_analytic

real (kind=4) mod_input_parameter::param_list::h_analytic

◆ half_sphere

logical mod_input_parameter::param_list::half_sphere

◆ hdf

character ( 128 ) mod_input_parameter::param_list::hdf

◆ hdfct

real ( kind=8 ) mod_input_parameter::param_list::hdfct

◆ height_dependent_dt

logical mod_input_parameter::param_list::height_dependent_dt

◆ hexcl

real ( kind=4 ) mod_input_parameter::param_list::hexcl

◆ hydro

logical mod_input_parameter::param_list::hydro

◆ ianalytic

logical mod_input_parameter::param_list::ianalytic

◆ ibootstrap

logical mod_input_parameter::param_list::ibootstrap

◆ iflex

logical mod_input_parameter::param_list::iflex

◆ ifpt

logical mod_input_parameter::param_list::ifpt

◆ ignore_exclusion

logical mod_input_parameter::param_list::ignore_exclusion

◆ ihom_charged_surf

logical mod_input_parameter::param_list::ihom_charged_surf

◆ iimg_chg

logical mod_input_parameter::param_list::iimg_chg

◆ imetaldesolv

logical mod_input_parameter::param_list::imetaldesolv

Special group for MetalDesolvation, distance_to_surface, energy_per_water, radius_patch, radius_water.

◆ initial_conf

integer mod_input_parameter::param_list::initial_conf

◆ ionerun

logical mod_input_parameter::param_list::ionerun

◆ ionic

real (kind=4) mod_input_parameter::param_list::ionic

analytic group, only HI and DH now, crowder later

◆ ionic_read

logical mod_input_parameter::param_list::ionic_read

◆ ipmf

logical mod_input_parameter::param_list::ipmf

Group for PMF calculations.

◆ irestart

logical mod_input_parameter::param_list::irestart

◆ irot

logical mod_input_parameter::param_list::irot

◆ isurf

logical mod_input_parameter::param_list::isurf

◆ itimestep

logical mod_input_parameter::param_list::itimestep

For timestep.

◆ list_conf_name

character ( 128 ) mod_input_parameter::param_list::list_conf_name

◆ lj_repf

character ( 128 ) mod_input_parameter::param_list::lj_repf

◆ ljf

character ( 128 ), dimension(:), allocatable mod_input_parameter::param_list::ljf

◆ ljfct

real ( kind=8 ) mod_input_parameter::param_list::ljfct

◆ ljrepfct

real ( kind=8 ) mod_input_parameter::param_list::ljrepfct

◆ lvol_rcut

real (kind=4) mod_input_parameter::param_list::lvol_rcut

◆ max_array_traj

integer mod_input_parameter::param_list::max_array_traj

◆ mem_traj_frames

integer mod_input_parameter::param_list::mem_traj_frames

◆ mentfi

integer mod_input_parameter::param_list::mentfi

◆ mentom

integer mod_input_parameter::param_list::mentom

◆ mentth

integer mod_input_parameter::param_list::mentth

◆ mentx

integer mod_input_parameter::param_list::mentx

◆ menty

integer mod_input_parameter::param_list::menty

◆ merge_step

integer mod_input_parameter::param_list::merge_step

◆ min_height

real ( kind=4 ) mod_input_parameter::param_list::min_height

◆ napt1

integer mod_input_parameter::param_list::napt1

◆ napt2

integer mod_input_parameter::param_list::napt2

◆ nb_cell_x

integer mod_input_parameter::param_list::nb_cell_x

◆ nb_cell_y

integer mod_input_parameter::param_list::nb_cell_y

◆ nb_cell_z

integer mod_input_parameter::param_list::nb_cell_z

◆ nb_contact

integer mod_input_parameter::param_list::nb_contact

◆ nb_lenjones

integer mod_input_parameter::param_list::nb_lenjones

◆ nb_solute

integer mod_input_parameter::param_list::nb_solute

◆ ncmx

integer mod_input_parameter::param_list::ncmx

◆ nearest_ngb

logical mod_input_parameter::param_list::nearest_ngb

◆ nnnons

integer mod_input_parameter::param_list::nnnons

◆ no_height_hi

logical mod_input_parameter::param_list::no_height_hi

◆ no_image_hi

logical mod_input_parameter::param_list::no_image_hi

◆ no_normal_hi

logical mod_input_parameter::param_list::no_normal_hi

◆ novers

integer mod_input_parameter::param_list::novers

◆ nrec

integer mod_input_parameter::param_list::nrec

◆ nrun

integer mod_input_parameter::param_list::nrun

◆ ntraj_rec

integer mod_input_parameter::param_list::ntraj_rec

◆ nwin

integer mod_input_parameter::param_list::nwin

◆ nwrec

integer mod_input_parameter::param_list::nwrec

◆ old_rotation

logical mod_input_parameter::param_list::old_rotation

◆ oneway_surf_chg

logical mod_input_parameter::param_list::oneway_surf_chg

◆ pair_proteins

logical mod_input_parameter::param_list::pair_proteins

◆ pbc

logical mod_input_parameter::param_list::pbc

◆ pdb_filename

character ( 128 ) mod_input_parameter::param_list::pdb_filename

For solute group.

◆ pfinish

real(kind=8) mod_input_parameter::param_list::pfinish

◆ probep

real ( kind=4 ) mod_input_parameter::param_list::probep

◆ probew

real ( kind=4 ) mod_input_parameter::param_list::probew

◆ pstart

real(kind=8) mod_input_parameter::param_list::pstart

◆ qef

character ( 128 ) mod_input_parameter::param_list::qef

◆ radius_read

logical mod_input_parameter::param_list::radius_read

◆ radw

real(kind=4) mod_input_parameter::param_list::radw

◆ rboost

real ( kind=4 ) mod_input_parameter::param_list::rboost

◆ real_net_charge

real ( kind=8 ) mod_input_parameter::param_list::real_net_charge

◆ record_startpos

logical mod_input_parameter::param_list::record_startpos

◆ rep_rad

real ( kind=8 ) mod_input_parameter::param_list::rep_rad

◆ restart_filename

character ( 128 ) mod_input_parameter::param_list::restart_filename

For restart.

◆ rmsd_min

real ( kind=8 ) mod_input_parameter::param_list::rmsd_min

For complexes and trajectories.

◆ rst_complex

logical mod_input_parameter::param_list::rst_complex

◆ rxna12f

character ( 128 ) mod_input_parameter::param_list::rxna12f

For reaction criteria.

◆ save_access

logical mod_input_parameter::param_list::save_access

◆ save_exclusion

integer mod_input_parameter::param_list::save_exclusion

◆ sdamd

integer mod_input_parameter::param_list::sdamd

◆ shift_rt_x

real ( kind=4) mod_input_parameter::param_list::shift_rt_x

◆ shift_rt_y

real ( kind=4) mod_input_parameter::param_list::shift_rt_y

◆ shift_rt_z

real ( kind=4) mod_input_parameter::param_list::shift_rt_z

◆ size_cell_x

real ( kind=4) mod_input_parameter::param_list::size_cell_x

◆ size_cell_y

real ( kind=4) mod_input_parameter::param_list::size_cell_y

◆ size_cell_z

real ( kind=4) mod_input_parameter::param_list::size_cell_z

◆ size_thread

integer mod_input_parameter::param_list::size_thread

◆ start_pos

real ( kind=4 ) mod_input_parameter::param_list::start_pos

◆ std_freq

real ( kind=4 ) mod_input_parameter::param_list::std_freq

◆ stop_traj

logical mod_input_parameter::param_list::stop_traj

◆ surf_geom

logical mod_input_parameter::param_list::surf_geom

◆ surface_charge_dens

real ( kind=8 ) mod_input_parameter::param_list::surface_charge_dens

◆ surface_height

real (kind=4) mod_input_parameter::param_list::surface_height

◆ surface_prefct

real (kind=4) mod_input_parameter::param_list::surface_prefct

◆ swd1

real ( kind=8 ) mod_input_parameter::param_list::swd1

◆ swd2

real ( kind=8 ) mod_input_parameter::param_list::swd2

◆ t_calc

type ( type_calculation ) mod_input_parameter::param_list::t_calc

For group type calculation.

◆ thresold

real ( kind=4 ) mod_input_parameter::param_list::thresold

◆ timemax

real ( kind=8 ) mod_input_parameter::param_list::timemax

◆ total_conf

integer mod_input_parameter::param_list::total_conf

For flexibility.

◆ total_grids

integer mod_input_parameter::param_list::total_grids

◆ total_solutes

integer mod_input_parameter::param_list::total_solutes

◆ traj_sum_nrj

logical mod_input_parameter::param_list::traj_sum_nrj

◆ type_geom

integer mod_input_parameter::param_list::type_geom

◆ vert_excl

logical mod_input_parameter::param_list::vert_excl

◆ vol_rad

real ( kind=8 ) mod_input_parameter::param_list::vol_rad

◆ win0

real ( kind=4 ) mod_input_parameter::param_list::win0

For rate claculation.

◆ xcent

real ( kind=8 ) mod_input_parameter::param_list::xcent

◆ xmax

real ( kind=4 ) mod_input_parameter::param_list::xmax

◆ xmin

real ( kind=4 ) mod_input_parameter::param_list::xmin

◆ ycent

real ( kind=8 ) mod_input_parameter::param_list::ycent

◆ ymax

real ( kind=4 ) mod_input_parameter::param_list::ymax

◆ ymin

real ( kind=4 ) mod_input_parameter::param_list::ymin

◆ zadw

real(kind=4) mod_input_parameter::param_list::zadw

◆ zcent

real ( kind=8 ) mod_input_parameter::param_list::zcent

◆ zmax

real ( kind=4 ) mod_input_parameter::param_list::zmax

◆ zmin

real ( kind=4 ) mod_input_parameter::param_list::zmin

The documentation for this type was generated from the following file:
Imprint/Privacy