SDA  7.1
Simulation of Diffusional Association
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Functions/Subroutines
MainLoop_sda_pmf.f90 File Reference

Loop for sda_pmf. More...

Functions/Subroutines

subroutine mainloop_sda_pmf (tab_protein, o_complexes, trajectories, param_force_energy, param_analytic, param_metaldesolv, param_pmf, geom, type_calc)
 Main function for sda_pmf. More...
 
subroutine compute_pmf (ent, n_theta, n_phi, n_psi, n_x, n_y, dA, dH_z, dS_z, partitionF_zcoord)
 Subroutine to compute the pmf value for a given z above the surface.
rotational and translation configurational distributions c and write occupation map (translational and rotational) norm to 1; dV=dT*dz- 3-dimentional space volume = zmax*4pi. More...
 
subroutine rotation_pmf_sda6 (rot, rotentfi, rotentth, rotentom)
 compute the rotation matrix for a given set of angles.

 
subroutine rotation_z1y2x3_tbryan (rot, rotentfi, rotentth, rotentom)
 To get an extrinsic rotation with correct angles.
 
subroutine rotation_z1x2z3 (rot, rotentfi, rotentth, rotentom)
 Try to follow wikipedia, z1x2z3.
 

Detailed Description

Loop for sda_pmf.

Version
{version 7.1 (2015)}

Copyright (c) 2009, 2010, 2015 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) formerly EML Research gGmbH (EML-R ) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

Copyright (c) 2000, 2003 European Molecular Biology Laboratory Meyerhofstr. 1, Postfach 10.2209 D-69012, 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/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


Function/Subroutine Documentation

subroutine compute_pmf ( real ( kind=8 ), dimension (:,:,:,:,:), intent(in)  ent,
integer, intent(in)  n_theta,
integer, intent(in)  n_phi,
integer, intent(in)  n_psi,
integer, intent(in)  n_x,
integer, intent(in)  n_y,
real ( kind=8 ), intent(in)  dA,
real ( kind=8 ), intent(out)  dH_z,
real ( kind=8 ), intent(out)  dS_z,
real ( kind=8 ), intent(in)  partitionF_zcoord 
)

Subroutine to compute the pmf value for a given z above the surface.
rotational and translation configurational distributions c and write occupation map (translational and rotational) norm to 1; dV=dT*dz- 3-dimentional space volume = zmax*4pi.

state_probability*dT*dz is the probability of finding the protein at Y+dT, Z+dz dH- change of enthalpy, dSt - change of translational entropy; dSr- rot entropy

Parameters
dAsurface area sampled along x/y, dA = dx * dy
dH_zreturn the local enthalpy, H = <U>
dS_zreturn the local entropy

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subroutine mainloop_sda_pmf ( type ( array_protein_type ), target  tab_protein,
type ( record )  o_complexes,
type ( record )  trajectories,
type ( type_force_energy )  param_force_energy,
type ( parameter_analytic )  param_analytic,
type ( parameter_metaldesolv )  param_metaldesolv,
type ( parameter_pmf )  param_pmf,
type ( geometry )  geom,
type ( type_calculation )  type_calc 
)

Main function for sda_pmf.

See the ProMetCS paper for the theory of the method:

ProMetCS: An Atomistic Force Field for Modeling Protein−Metal Surface Interactions in a Continuum Aqueous Solvent Daria B. Kokh, Stefano Corni, Peter J. Winn, Martin Hoefling, Kay E. Gottschalk, and Rebecca C. Wade Journal of Chemical Theory and Computation 2010 6 (5), 1753-1768.

The entropic terms are computed using the method described in:

Association Entropy in Adsorption Processes Nir Ben-Tal, Barry Honig, Carey K. Bagdassarian and Avinoam Ben-Shaul Biophysical Journal 2000 79, 1180-1187.

This version tries to run everything in one parallel loop to
avoid the allocation/deallocation/copy of tab_proteins and array energy

In this version use section and nested loop (to activate in main.f90)
use nested parallel do in comp_pmf
Loose energymin to avoid CRITICAL section, provided in trajectory

Flexibility is not implemented.

Parameters
tab_protein: instance of array_protein_type
o_complexes: instance of record for complexes output
trajectories: instance of record for trajectory output
param_force_energy: instance of type_force_energy
param_analytic: structure parameter_analytic
geom: instance of geometry
type_calc: instance of type_calculation
p_restart: pointer to the restart file

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