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//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2020 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library is distributed in the hope that it will be useful, but WITHOUT
// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
#include <boost/test/unit_test.hpp>
#include <ost/mol/mm/settings.hh>
#include <ost/mol/mm/forcefield.hh>
#include <ost/mol/mm/interaction.hh>
#include <ost/mol/mm/buildingblock.hh>
#include <ost/mol/mm/gromacs_block_modifiers.hh>
#include <ost/message.hh>
#include <ost/mol/builder.hh>
#include <ost/mol/xcs_editor.hh>
#include <ost/io/mol/pdb_reader.hh>
#include <ost/mol/mm/simulation.hh>
#include <ost/mol/mm/topology.hh>
#include <OpenMM.h>
using namespace ost::mol::mm;
BOOST_AUTO_TEST_SUITE( mol_mm );
BOOST_AUTO_TEST_CASE(test_simulation_basics){
String pdb_name = "1CRN.pdb";
ost::io::PDBReader reader(pdb_name, ost::io::IOProfile());
ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
reader.Import(test_ent);
ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor);
processor->Process(test_ent);
SettingsPtr settings(new Settings);
ForcefieldPtr forcefield = Forcefield::Load("CHARMM27.dat");
settings->forcefield = forcefield;
settings->add_gbsa = true;
TopologyPtr top = TopologyCreator::Create(test_ent,settings);
//lets add interactions, that are not set when using charmm
top->AddHarmonicAngle(1,2,3,1.0,10.0);
top->AddPeriodicImproper(1,2,3,4,2,1.0,10.0);
top->AddDistanceConstraint(1,2,10.0);
top->AddHarmonicPositionRestraint(1,geom::Vec3(0.0,0.0,0.0),10.0);
top->AddHarmonicDistanceRestraint(1,2,10.0,10.0);
settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.002));
Simulation sim(top, test_ent, settings);
//we check, wether the reset functions have the desired effect on the topology
//we cannot really check the effect on the openmm system...
sim.ResetHarmonicBond(42,5.0,6.0);
sim.ResetHarmonicAngle(0,2.0,9.0);
sim.ResetUreyBradleyAngle(42,2.0,6.0,7.0,8.0);
sim.ResetPeriodicDihedral(42,4,2.0,6.0);
sim.ResetPeriodicImproper(0,5,2.0,9.0);
sim.ResetHarmonicImproper(42,2.0,6.0);
sim.ResetLJPair(42,5.0,6.0);
sim.ResetDistanceConstraint(0,10.0);
sim.ResetHarmonicPositionRestraint(0,geom::Vec3(1.0,1.0,1.0),5.0);
sim.ResetHarmonicDistanceRestraint(0,5.0,10.0);
sim.ResetLJ(42,2.0,3.0);
sim.ResetGBSA(42,5.0,6.0);
sim.ResetCharge(42,100.0);
sim.ResetMass(42,200.0);
uint ui1,ui2,ui3,ui4;
int i1;
Real r1,r2,r3,r4;
geom::Vec3 pos;
top->GetHarmonicBondParameters(42,ui1,ui2,r1,r2);
BOOST_CHECK(r1 == 5.0 && r2 == 6.0);
top->GetHarmonicAngleParameters(0,ui1,ui2,ui3,r1,r2);
BOOST_CHECK(r1 == 2.0 && r2 == 9.0);
top->GetUreyBradleyAngleParameters(42,ui1,ui2,ui3,r1,r2,r3,r4);
BOOST_CHECK(r1 == 2.0 && r2 == 6.0 && r3 == 7.0 && r4 == 8.0);
top->GetPeriodicDihedralParameters(42,ui1,ui2,ui3,ui4,i1,r1,r2);
BOOST_CHECK(i1 == 4 && r1 == 2.0 && r2 == 6.0);
top->GetPeriodicImproperParameters(0,ui1,ui2,ui3,ui4,i1,r1,r2);
BOOST_CHECK(i1 == 5 && r1 == 2.0 && r2 == 9.0);
top->GetLJPairParameters(42,ui1,ui2,r1,r2);
BOOST_CHECK(r1 == 5.0 && r2 == 6.0);
top->GetDistanceConstraintParameters(0,ui1,ui2,r1);
BOOST_CHECK(r1 == 10.0);
top->GetHarmonicPositionRestraintParameters(0, ui1, pos,r1, r2, r3, r3);
BOOST_CHECK(pos == geom::Vec3(1.0,1.0,1.0) && r1 == 5.0);
top->GetHarmonicDistanceRestraintParameters(0,ui1,ui2, r1, r2);
BOOST_CHECK(r1 == 5.0 && r2 == 10.0);
r1 = top->GetSigma(42);
r2 = top->GetEpsilon(42);
BOOST_CHECK(r1 == 2.0 && r2 == 3.0);
r1 = top->GetGBSARadius(42);
r2 = top->GetOBCScaling(42);
BOOST_CHECK(r1 == 5.0 && r2 == 6.0);
r1 = top->GetCharge(42);
r2 = top->GetMass(42);
BOOST_CHECK(r1 == 100.0 && r2 == 200.0);
}
BOOST_AUTO_TEST_CASE(test_simulation_energy_calculations){
String pdb_name = "1CRN.pdb";
ost::io::PDBReader reader(pdb_name, ost::io::IOProfile());
ost::mol::EntityHandle test_ent = ost::mol::CreateEntity();
reader.Import(test_ent);
ost::conop::ProcessorPtr processor(new ost::conop::HeuristicProcessor);
processor->Process(test_ent);
SettingsPtr settings(new Settings);
ForcefieldPtr forcefield = Forcefield::Load("CHARMM27.dat");
settings->forcefield = forcefield;
TopologyPtr top = TopologyCreator::Create(test_ent,settings);
//lets add interactions, that are not set when using charmm
settings->integrator = IntegratorPtr(new OpenMM::VerletIntegrator(0.002));
Simulation sim(top, test_ent,settings);
sim.ApplySD(1.0, 200);
//the energy values have been compared with the results from the
//CHARMM27 forcefield in gromacs
//differenecs in energy(kJ/mol):
//harmonic_bond: 0.00021344800001
//urey_bradley_angle: 0.00021319300003
//periodic_dihedral: 0.00018275799993
//harmonic_improper: 0.00001410630000
//cmap: 0.00192255100001
//nonbonded: 0.00204422999968
//You'll most likely get different results when repeating the comparison with gromacs
//this is because of the precision.
//Right now we have full real precision in the positions.
//When you write down the pdb, precision will be lowered to 3 digits.
//Another digit gets lost, when you create a gromacs topology...
//Gromacs writes down the positions using nm instead of A, but
//also has a precision of 3 digits.
// Threshold is relatively permissive (1e-1->0.1% difference) depending on
// OpenMM version / Hardware you might get slightly different results.
// Error propagates when performing 200 steps steepest descent (minimizes from
// roughly 1981 down to -2381).
BOOST_CHECK_CLOSE(sim.GetPotentialEnergy(), -2381.24, Real(1e-1));
}
BOOST_AUTO_TEST_SUITE_END();
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