MainLoop_sda_pmf.f90 File Reference

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.
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.
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

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

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Loop for sda_pmf

Function/Subroutine Documentation

compute_pmf()

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

dA	surface area sampled along x/y, dA = dx * dy
dH_z	return the local enthalpy, H =
dS_z	return the local entropy

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mainloop_sda_pmf()

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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rotation_pmf_sda6()

subroutine rotation_pmf_sda6	(	real ( kind=8 ), dimension ( 3,3 ), intent(inout)	rot,
		real ( kind=8 ), intent(in)	rotentfi,
		real ( kind=8 ), intent(in)	rotentth,
		real ( kind=8 ), intent(in)	rotentom
	)

compute the rotation matrix for a given set of angles.

rotation_z1x2z3()

subroutine rotation_z1x2z3	(	real ( kind=8 ), dimension ( 3,3 ), intent(out)	rot,
		real ( kind=8 ), intent(in)	rotentfi,
		real ( kind=8 ), intent(in)	rotentth,
		real ( kind=8 ), intent(in)	rotentom
	)

Try to follow wikipedia, z1x2z3.

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rotation_z1y2x3_tbryan()

subroutine rotation_z1y2x3_tbryan	(	real ( kind=8 ), dimension ( 3,3 ), intent(out)	rot,
		real ( kind=8 ), intent(in)	rotentfi,
		real ( kind=8 ), intent(in)	rotentth,
		real ( kind=8 ), intent(in)	rotentom
	)

To get an extrinsic rotation with correct angles.