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| subroutine | mod_compute_analytic_2proteins::force_analytic_dh (tab_protein, param_force_energy, dist, f, t, t1) |
| | Compute force with analytic function.
Values precomputed and stored in an array Seems necessary to make separate for dh ? easier.
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| subroutine | mod_compute_analytic_2proteins::pair_force_full_analytic_2proteins (prot1, prot2, type_p1, type_p2, dist, ff2, ff1) |
| | Compute force if solute and grids do not overlap p2 solute in DH "grid" of p1, and opposite.
.
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| subroutine | mod_compute_analytic_2proteins::pair_force_partial_analytic_2proteins (prot1, prot2, type_p1, type_p2, dist, ff2, ff1, tt2, tt1) |
| | Only partial analytic, loop over all atoms in this case Analytic is set to zero if inside the cutoff.
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| subroutine | mod_compute_analytic_2proteins::energy_analytic_dh (tab_protein, param_force_energy, dist, array_energy) |
| | Compute energy with analytic function Seems necessary to make separate for dh ? easier.. to see later.
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| subroutine | mod_compute_analytic_2proteins::pair_energy_full_analytic_2proteins (prot1, prot2, type_p1, type_p2, dist, energy1, energy2) |
| | Compute Full DH interactions.
Need to split, cutoffs may be different/ asymetric between p1 and p2.
Only compute El-DH prot1 in analytical grid of protein 2 ( all grids stored in prot2 % p_sogrid % pset_analytical) Not good for 2 proteins because asymetry between static/mobil solute Need to test cutoffs for each interaction.
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| subroutine | mod_compute_analytic_2proteins::pair_energy_partial_analytic (prot1, prot2, type_p1, type_p2, dist, energy1, energy2) |
| | Only partial analytic, loop over all atoms in this case.
Analytic has been set to zero if inside the grid Asymetry due to cutoffs.
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| subroutine | mod_compute_analytic_2proteins::force_analytic_dh_imgchg (tab_protein, param_force_energy, dist, f, t) |
| | Compute forces for image charge DH routine NJB: Changed to move reflection plane to edge atomic layer when surface more than one atom.
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| subroutine | mod_compute_analytic_2proteins::force_full_analytic_dh_imgchg (prot2, type_p2, dist, mirror_z, ff_analytic) |
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| subroutine | mod_compute_analytic_2proteins::force_partial_analytic_dh_imgchg (prot2, type_p2, dist, mirror_z, ff_partial, tt_partial) |
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| subroutine | mod_compute_analytic_2proteins::energy_analytic_dh_imgchg (tab_protein, param_force_energy, dist, array_energy) |
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| subroutine | mod_compute_analytic_2proteins::energy_full_analytic_dh_imgchg (prot2, type_p2, dist, mirror_z, energy2_analytic) |
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| subroutine | mod_compute_analytic_2proteins::energy_partial_analytic_dh_imgchg (prot2, type_p2, dist, mirror_z, energy2_partial) |
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| subroutine | mod_compute_analytic_2proteins::force_analytic_hom_charged_surf (tab_protein, param_force_energy, dist, f, t) |
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| subroutine | mod_compute_analytic_2proteins::force_full_analytic_hom_charged_surf (prot1, prot2, type_p2, dist, ff_analytic) |
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| subroutine | mod_compute_analytic_2proteins::force_partial_analytic_hom_charged_surf (prot1, prot2, type_p2, dist, ff_partial, tt_partial) |
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| subroutine | mod_compute_analytic_2proteins::energy_analytic_hom_charged_surf (tab_protein, param_force_energy, dist, array_energy) |
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| subroutine | mod_compute_analytic_2proteins::energy_full_analytic_hom_charged_surf (prot1, prot2, type_p2, dist, energy2_analytic) |
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| subroutine | mod_compute_analytic_2proteins::energy_partial_analytic_hom_charged_surf (prot1, prot2, type_p2, dist, energy2_partial) |
| |
- 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
Compute force and energies for analytic interaction (DH for now) for sda_2proteins.
1.9.8
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