SDA (SDA flex)  7.2
Simulation of Diffusional Association
Functions/Subroutines
make_edhdlj_grid.f90 File Reference

Functions/Subroutines

program make_edhdlj_grid
 Prgram make_edhdlj_grid. More...
 
subroutine read_input (name_input, grid_type, parameters)
 Read specific input file for the grids. More...
 
subroutine compute_ed (grid, list_atom, a2, a3, parameters)
 Compute electrostatic desolvation. More...
 
subroutine compute_hd (grid, list_atom, array_van, parameters)
 Compute apolar desolvation. More...
 
subroutine compute_ljrep (grid, list_atom, array_van, parameters)
 Compute soft-core (repulsive lennard-jones) More...
 
subroutine dipole (list_atom, a2, a3, grid_pos, parameters, energy)
 Used for electrostic desovaltion computation. More...
 
subroutine hdenergy (list_atom, grid_pos, array_van, parameters, energy)
 Use for apolar desolvation computation. More...
 
subroutine ljrep_energy (list_atom, array_van, grid_pos, parameters, energy)
 Use for repulsive lennard-jones computation. More...
 

Detailed Description

Version
{version 7.2.3 (2019)}

Copyright (c) 2009, 2010, 2015, 2016, 2019 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

Please send your contact address to get information on updates and new features to "mcmsoft@h-its.org". Questions will be answered as soon as possible.

References: see also http://mcm.h-its.org/sda7/do:c/doc_sda7/references.html:

Brownian dynamics simulation of protein-protein diffusional encounter. (1998) Methods, 14, 329-341.

SDA 7: A modular and parallel implementation of the simulation of diffusional association software. Journal of computational chemistry 36.21 (2015): 1631-1645.

Authors: M.Martinez, N.J.Bruce, J.Romanowska, D.B.Kokh, P.Mereghetti, X. Yu, M. Ozboyaci, M. Reinhardt, P. Friedrich, R.R.Gabdoulline, S.Richter and R.C.Wade


Create electrostatic desolvation, apolar desolvation and repulsive lennard-jones grids

Function/Subroutine Documentation

◆ compute_ed()

subroutine compute_ed ( type ( type_grid grid,
real ( kind = 8 ), dimension ( :, : ), intent(in)  list_atom,
real ( kind=8 ), dimension ( : )  a2,
real ( kind=8 ), dimension ( : )  a3,
type ( param_list_tools ), intent(in)  parameters 
)

Compute electrostatic desolvation.

Here is the call graph for this function:
Here is the caller graph for this function:

◆ compute_hd()

subroutine compute_hd ( type ( type_grid grid,
real ( kind = 8 ), dimension ( :, : ), intent(in)  list_atom,
real ( kind = 8 ), dimension ( : ), intent(in)  array_van,
type ( param_list_tools ), intent(in)  parameters 
)

Compute apolar desolvation.

Here is the call graph for this function:
Here is the caller graph for this function:

◆ compute_ljrep()

subroutine compute_ljrep ( type ( type_grid grid,
real ( kind = 8 ), dimension ( :, : ), intent(in)  list_atom,
real ( kind = 8 ), dimension ( : ), intent(in)  array_van,
type ( param_list_tools ), intent(in)  parameters 
)

Compute soft-core (repulsive lennard-jones)

Here is the call graph for this function:
Here is the caller graph for this function:

◆ dipole()

subroutine dipole ( real ( kind = 8 ), dimension ( :, : ), intent(in)  list_atom,
real ( kind=8 ), dimension ( : ), intent(in)  a2,
real ( kind=8 ), dimension ( : ), intent(in)  a3,
real ( kind=8 ), dimension ( 3 ), intent(in)  grid_pos,
type ( param_list_tools ), intent(in)  parameters,
real ( kind=8 ), intent(out)  energy 
)

Used for electrostic desovaltion computation.

Here is the caller graph for this function:

◆ hdenergy()

subroutine hdenergy ( real ( kind = 8 ), dimension ( :, : ), intent(in)  list_atom,
real ( kind=8 ), dimension ( 3 ), intent(in)  grid_pos,
real ( kind = 8 ), dimension ( : ), intent(in)  array_van,
type ( param_list_tools parameters,
real ( kind=8 ), intent(out)  energy 
)

Use for apolar desolvation computation.

Here is the caller graph for this function:

◆ ljrep_energy()

subroutine ljrep_energy ( real ( kind = 8 ), dimension ( :, : ), intent(in)  list_atom,
real ( kind = 8 ), dimension ( : ), intent(in)  array_van,
real ( kind=8 ), dimension ( 3 ), intent(in)  grid_pos,
type ( param_list_tools ), intent(in)  parameters,
real ( kind=8 ), intent(out)  energy 
)

Use for repulsive lennard-jones computation.

Here is the caller graph for this function:

◆ read_input()

subroutine read_input ( character *128, intent(in)  name_input,
integer, intent(in)  grid_type,
type ( param_list_tools ), intent(out)  parameters 
)

Read specific input file for the grids.

Parameters
name_input: file name of the input
grid_type: integer for the grid_type, refer to mod_gridtype
parameters: specific parameters for tools param_list_tools
Here is the caller graph for this function:
Imprint/Privacy