Define the timestep ( variable for sda_2proteins ) More...
Functions/Subroutines | |
subroutine | init_time (param_timestep, geom, dist, rhit, dm30, dtnow, hit) |
Define instantaneous timestep if it is variable ( only for sda_2proteins ) . More... | |
subroutine | check_timestep (geom, param_timestep, tab_protein) |
Compute basic property about the maximum timestep... More... | |
Define the timestep ( variable for sda_2proteins )
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References (see also http://mcm.h-its.org/sda7/doc/doc_sda7/references.html):
Brownian dynamics simulation of protein-protein diffusional encounter.
(1998) Methods, 14, 329-341.
Authors: M.Martinez, N.J.Bruce, J.Romanowska, D.B.Kokh, P.Mereghetti, R.R.Gabdoulline, M. Ozboyaci, S.Richter and R.C.Wade
subroutine check_timestep | ( | type ( geometry ) | geom, |
type ( parameter_timestep ) | param_timestep, | ||
type ( array_protein_type ) | tab_protein | ||
) |
Compute basic property about the maximum timestep...
geom | : instance of mod_geometry |
param_timestep | : structure for the timestep varaibles |
tab_protein | : intance of mod_array_protein |
subroutine init_time | ( | type ( parameter_timestep ), intent(in) | param_timestep, |
type ( geometry ), intent(in) | geom, | ||
real ( kind=4 ), intent(in) | dist, | ||
real ( kind=4 ), intent(in) | rhit, | ||
real ( kind=8 ), intent(in) | dm30, | ||
real ( kind=8 ), intent(out) | dtnow, | ||
logical, intent(out) | hit | ||
) |
Define instantaneous timestep if it is variable ( only for sda_2proteins )
.
Depends on position and geometry
Reduce time step near outer boundary
Small difference with sda 6 implementation (value of dthet)
param_timestep | : structure of timestep parameters |
geom | : instance of geometry |
dist | : distance between solutes |
rhit | : distance where overlap is possible |
dm30 | : diff. coeff. * 30 |
dtnow | : return timestep |
hit | : return if overlap is possible at this distance |