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... | |
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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
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.
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.
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)
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.
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.
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.
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.
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 |