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|
// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#include <BALL/CONCEPT/classTest.h>
#include <BALLTestConfig.h>
///////////////////////////
#include <BALL/MOLMEC/CHARMM/charmm.h>
#include <BALL/MOLMEC/CHARMM/charmmNonBonded.h>
#include <BALL/MOLMEC/CHARMM/charmmBend.h>
#include <BALL/MOLMEC/CHARMM/charmmStretch.h>
#include <BALL/MOLMEC/CHARMM/charmmTorsion.h>
#include <BALL/MOLMEC/CHARMM/charmmImproperTorsion.h>
#include <BALL/FORMAT/PDBFile.h>
#include <BALL/FORMAT/HINFile.h>
#include <BALL/STRUCTURE/defaultProcessors.h>
#include <BALL/STRUCTURE/fragmentDB.h>
///////////////////////////
START_TEST(CharmmFF)
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
using namespace BALL;
CharmmFF* charmm;
CHECK(CharmmFF())
charmm = new CharmmFF();
TEST_NOT_EQUAL(charmm, 0)
RESULT
CHECK(~CharmmFF())
delete charmm;
RESULT
CHECK(CharmmFF(const CharmmFF& force_field))
CharmmFF a1;
CharmmFF a2(a1);
RESULT
CHECK(specificSetup())
CharmmFF a;
a.specificSetup();
RESULT
FragmentDB frag_db("fragments/Fragments.db");
{
// read the PDB file containing a single GLY
PDBFile f(BALL_TEST_DATA_PATH(CharmmFF_test_1.pdb));
System s;
f >> s;
f.close();
// normalize the names and build the bonds
s.apply(frag_db.normalize_names);
s.apply(frag_db.build_bonds);
// setup the force field
Options options;
options[CharmmFF::Option::ASSIGN_CHARGES] = "true";
options[CharmmFF::Option::ASSIGN_TYPENAMES] = "true";
options[CharmmFF::Option::ASSIGN_TYPES] = "true";
options[CharmmFF::Option::FILENAME] = "CHARMM/EEF1/param19_eef1.ini";
CharmmFF eef1(s, options);
CHECK(energy test 1 (GLY) [EEF1])
// check whether we got the right number of atoms
TEST_EQUAL(s.countAtoms(), 8)
eef1.updateEnergy();
PRECISION(5e-3)
TEST_REAL_EQUAL(eef1.getEnergy(), 157.4572251)
TEST_REAL_EQUAL(eef1.getStretchEnergy(), 30.83411352)
TEST_REAL_EQUAL(eef1.getBendEnergy(), 307.4544619)
TEST_REAL_EQUAL(eef1.getProperTorsionEnergy(), 2.11036776)
TEST_REAL_EQUAL(eef1.getImproperTorsionEnergy(), 5.48237888)
TEST_REAL_EQUAL(eef1.getTorsionEnergy(), 7.59275)
TEST_REAL_EQUAL(eef1.getVdWEnergy(), 26.64563664)
TEST_REAL_EQUAL(eef1.getESEnergy(), -53.3215644)
TEST_REAL_EQUAL(eef1.getSolvationEnergy(), -161.7481263)
RESULT
CHECK(gradient test 1 (GLY) [EEF1])
eef1.updateForces();
PRECISION(5e-3)
TEST_REAL_EQUAL(eef1.getRMSGradient(), 219.2263702)
RESULT
CHECK(force test 1 (GLY, stretch only) [EEF1])
// remove all components except for stretches
eef1.removeComponent("CHARMM NonBonded");
eef1.removeComponent("CHARMM Torsion");
eef1.removeComponent("CHARMM ImproperTorsion");
eef1.removeComponent("CHARMM Bend");
eef1.options[CharmmFF::Option::FILENAME] = "CHARMM/EEF1/param19_eef1.ini";
eef1.setup(s, options);
eef1.updateForces();
eef1.updateEnergy();
TEST_REAL_EQUAL(eef1.getEnergy(), 30.83411352)
TEST_REAL_EQUAL(eef1.getBendEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getProperTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getImproperTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getStretchEnergy(), 30.83411352)
TEST_REAL_EQUAL(eef1.getESEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getVdWEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getSolvationEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getRMSGradient(), 134.2599576)
Size i = 0;
Vector3 force;
AtomIterator atom_it = s.beginAtom();
for (; +atom_it; ++atom_it, ++i)
{
switch (i)
{
// values are taken from CHARMM calculaction
// (version 27b1 with param19_eef1.inp and toph19_eef1.inp,
// with modified nonbonded: atom rdiel cutnb 20. cutonnb 11. cutofnb 15.)
case 0: force = Vector3( 26.44796, 91.42712, -23.82851); break;
case 1: force = Vector3( 14.55307, 1.84307, -19.22059); break;
case 2: force = Vector3(-14.56795, -89.42944, 62.77158); break;
case 3: force = Vector3(-16.84492, -12.50059, -5.06838); break;
case 4: force = Vector3( -8.71000, 3.45793, -15.72975); break;
case 5: force = Vector3( -1.06629, -17.55152, -0.53075); break;
case 6: force = Vector3( 19.60441, 12.80711, 11.19068); break;
case 7: force = Vector3(-19.41627, 9.94631, -9.58428);
}
force = force - atom_it->getForce() * Constants::NA * 1e-13 / -4.184;
TEST_REAL_EQUAL(force.getLength(), 0.0)
}
RESULT
}
{
// read the PDB file containing a single GLY
PDBFile f(BALL_TEST_DATA_PATH(CharmmFF_test_1.pdb));
System s;
f >> s;
f.close();
// normalize the names and build the bonds
s.apply(frag_db.normalize_names);
s.apply(frag_db.build_bonds);
// setup the force field
Options options;
options[CharmmFF::Option::ASSIGN_CHARGES] = "true";
options[CharmmFF::Option::ASSIGN_TYPENAMES] = "true";
options[CharmmFF::Option::ASSIGN_TYPES] = "true";
options[CharmmFF::Option::FILENAME] = "CHARMM/EEF1/param19_eef1.ini";
CharmmFF eef1(s, options);
CHECK(energy test 2 (GLY) [EEF1])
// check whether we got the right number of atoms
TEST_EQUAL(s.countAtoms(), 8)
eef1.updateEnergy();
PRECISION(5e-3)
TEST_REAL_EQUAL(eef1.getEnergy(), 157.4572251)
TEST_REAL_EQUAL(eef1.getStretchEnergy(), 30.83411352)
TEST_REAL_EQUAL(eef1.getBendEnergy(), 307.4544619)
TEST_REAL_EQUAL(eef1.getProperTorsionEnergy(), 2.11036776)
TEST_REAL_EQUAL(eef1.getImproperTorsionEnergy(), 5.48237888)
TEST_REAL_EQUAL(eef1.getTorsionEnergy(), 7.59275)
TEST_REAL_EQUAL(eef1.getVdWEnergy(), 26.64563664)
TEST_REAL_EQUAL(eef1.getESEnergy(), -53.3215644)
TEST_REAL_EQUAL(eef1.getSolvationEnergy(), -161.7481263)
RESULT
CHECK(multiple calls to setup)
eef1.setup(s, options);
RESULT
CHECK(energy test 3 (GLY) [EEF1])
// check whether we got the right number of atoms
TEST_EQUAL(s.countAtoms(), 8)
eef1.updateEnergy();
PRECISION(5e-3)
TEST_REAL_EQUAL(eef1.getEnergy(), 157.4572251)
TEST_REAL_EQUAL(eef1.getStretchEnergy(), 30.83411352)
TEST_REAL_EQUAL(eef1.getBendEnergy(), 307.4544619)
TEST_REAL_EQUAL(eef1.getProperTorsionEnergy(), 2.11036776)
TEST_REAL_EQUAL(eef1.getImproperTorsionEnergy(), 5.48237888)
TEST_REAL_EQUAL(eef1.getTorsionEnergy(), 7.59275)
TEST_REAL_EQUAL(eef1.getVdWEnergy(), 26.64563664)
TEST_REAL_EQUAL(eef1.getESEnergy(), -53.3215644)
TEST_REAL_EQUAL(eef1.getSolvationEnergy(), -161.7481263)
RESULT
CHECK(multiple calls to setup/2)
eef1.setup(s, options);
RESULT
CHECK(energy test 4 (GLY) [EEF1])
// check whether we got the right number of atoms
TEST_EQUAL(s.countAtoms(), 8)
eef1.updateEnergy();
PRECISION(5e-3)
TEST_REAL_EQUAL(eef1.getEnergy(), 157.4572251)
TEST_REAL_EQUAL(eef1.getStretchEnergy(), 30.83411352)
TEST_REAL_EQUAL(eef1.getBendEnergy(), 307.4544619)
TEST_REAL_EQUAL(eef1.getProperTorsionEnergy(), 2.11036776)
TEST_REAL_EQUAL(eef1.getImproperTorsionEnergy(), 5.48237888)
TEST_REAL_EQUAL(eef1.getTorsionEnergy(), 7.59275)
TEST_REAL_EQUAL(eef1.getVdWEnergy(), 26.64563664)
TEST_REAL_EQUAL(eef1.getESEnergy(), -53.3215644)
TEST_REAL_EQUAL(eef1.getSolvationEnergy(), -161.7481263)
RESULT
}
CHECK(force test 2 (GLY, bend only) [EEF1])
// read the PDB file containing a single GLY
PDBFile f(BALL_TEST_DATA_PATH(CharmmFF_test_1.pdb));
System s;
f >> s;
f.close();
// check whether we got the right number of atoms
TEST_EQUAL(s.countAtoms(), 8)
// normalize the names and build the bonds
s.apply(frag_db.normalize_names);
s.apply(frag_db.build_bonds);
CharmmFF eef1;
// remove all components excecpt for bends
eef1.removeComponent("CHARMM Torsion");
eef1.removeComponent("CHARMM ImproperTorsion");
eef1.removeComponent("CHARMM NonBonded");
eef1.removeComponent("CHARMM Stretch");
eef1.options[CharmmFF::Option::ASSIGN_CHARGES] = "true";
eef1.options[CharmmFF::Option::ASSIGN_TYPENAMES] = "true";
eef1.options[CharmmFF::Option::ASSIGN_TYPES] = "true";
eef1.options[CharmmFF::Option::FILENAME] = "CHARMM/EEF1/param19_eef1.ini";
eef1.setup(s);
eef1.updateForces();
eef1.updateEnergy();
TEST_REAL_EQUAL(eef1.getEnergy(), 307.4544619)
TEST_REAL_EQUAL(eef1.getBendEnergy(), 307.4544619)
TEST_REAL_EQUAL(eef1.getProperTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getImproperTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getStretchEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getESEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getVdWEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getSolvationEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getRMSGradient(), 123.0344948)
Size i = 0;
Vector3 force;
AtomIterator atom_it = s.beginAtom();
for (; +atom_it; ++atom_it, ++i)
{
switch (i)
{
// values are taken from CHARMM calculaction
// (version 27b1 with param19_eef1.inp and toph19_eef1.inp,
// with modified nonbonded: atom rdiel cutnb 20. cutonnb 11. cutofnb 15.)
case 0: force = Vector3( 32.09360, -8.83321, 1.72968); break;
case 1: force = Vector3( 0.27122, -7.58892, -0.52235); break;
case 2: force = Vector3(-21.60332, -81.70418, 44.97363); break;
case 3: force = Vector3(-33.70472, 65.80094, -50.27192); break;
case 4: force = Vector3( 24.59176, 32.71333, 3.56059); break;
case 5: force = Vector3( -4.89956, 20.53095, 2.43037); break;
case 6: force = Vector3( 6.60390, -11.26640, 1.32471); break;
case 7: force = Vector3( -3.35288, -9.65251, -3.22471);
}
force = force - atom_it->getForce() * Constants::NA * 1e-13 / -4.184;
TEST_REAL_EQUAL(force.getLength(), 0.0)
}
RESULT
CHECK(force test 3 (GLY, torsion only) [EEF1])
// read the PDB file containing a single GLY
PDBFile f(BALL_TEST_DATA_PATH(CharmmFF_test_1.pdb));
System s;
f >> s;
f.close();
// check whether we got the right number of atoms
TEST_EQUAL(s.countAtoms(), 8)
// normalize the names and build the bonds
s.apply(frag_db.normalize_names);
s.apply(frag_db.build_bonds);
CharmmFF eef1;
// remove all components excecpt for proper torsions
eef1.removeComponent("CHARMM Bend");
eef1.removeComponent("CHARMM ImproperTorsion");
eef1.removeComponent("CHARMM NonBonded");
eef1.removeComponent("CHARMM Stretch");
eef1.options[CharmmFF::Option::ASSIGN_CHARGES] = "true";
eef1.options[CharmmFF::Option::ASSIGN_TYPENAMES] = "true";
eef1.options[CharmmFF::Option::ASSIGN_TYPES] = "true";
eef1.options[CharmmFF::Option::FILENAME] = "CHARMM/EEF1/param19_eef1.ini";
eef1.setup(s);
eef1.updateForces();
eef1.updateEnergy();
TEST_REAL_EQUAL(eef1.getEnergy(), 2.11036776)
TEST_REAL_EQUAL(eef1.getBendEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getProperTorsionEnergy(), 2.11036776)
TEST_REAL_EQUAL(eef1.getImproperTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getTorsionEnergy(), 2.11036776)
TEST_REAL_EQUAL(eef1.getStretchEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getESEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getVdWEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getSolvationEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getRMSGradient(), 4.60127032)
Size i = 0;
Vector3 force;
AtomIterator atom_it = s.beginAtom();
for (; +atom_it; ++atom_it, ++i)
{
switch (i)
{
// values are taken from CHARMM calculaction
// (version 27b1 with param19_eef1.inp and toph19_eef1.inp,
// with modified nonbonded: atom rdiel cutnb 20. cutonnb 11. cutofnb 15.)
case 0: force = Vector3(-1.03592, 0.56305, 1.01054); break;
case 1: force = Vector3(-0.29165, -0.83152, -0.30056); break;
case 2: force = Vector3( 2.52092, 0.25830, -1.49679); break;
case 3: force = Vector3(-0.58905, 0.51427, 0.68932); break;
case 4: force = Vector3(-2.73842, -1.08243, 1.15208); break;
case 5: force = Vector3( 2.13412, 0.57834, -1.05459); break;
case 6: force = Vector3( 0.00000, 0.00000, 0.00000); break;
case 7: force = Vector3( 0.00000, 0.00000, 0.00000);
}
force = force - atom_it->getForce() * Constants::NA * 1e-13 / -4.184;
TEST_REAL_EQUAL(force.getLength(), 0.0)
}
RESULT
CHECK(force test 4 (GLY, improper torsion only) [EEF1])
// read the PDB file containing a single GLY
PDBFile f(BALL_TEST_DATA_PATH(CharmmFF_test_1.pdb));
System s;
f >> s;
f.close();
// check whether we got the right number of atoms
TEST_EQUAL(s.countAtoms(), 8)
// normalize the names and build the bonds
s.apply(frag_db.normalize_names);
s.apply(frag_db.build_bonds);
CharmmFF eef1;
// remove all components excecpt for proper torsions
eef1.removeComponent("CHARMM Bend");
eef1.removeComponent("CHARMM Torsion");
eef1.removeComponent("CHARMM NonBonded");
eef1.removeComponent("CHARMM Stretch");
eef1.options[CharmmFF::Option::ASSIGN_CHARGES] = "true";
eef1.options[CharmmFF::Option::ASSIGN_TYPENAMES] = "true";
eef1.options[CharmmFF::Option::ASSIGN_TYPES] = "true";
eef1.options[CharmmFF::Option::FILENAME] = "CHARMM/EEF1/param19_eef1.ini";
eef1.setup(s);
eef1.updateForces();
eef1.updateEnergy();
TEST_REAL_EQUAL(eef1.getEnergy(), 5.48237888)
TEST_REAL_EQUAL(eef1.getBendEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getProperTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getImproperTorsionEnergy(), 5.48237888)
TEST_REAL_EQUAL(eef1.getTorsionEnergy(), 5.48237888)
TEST_REAL_EQUAL(eef1.getStretchEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getESEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getVdWEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getSolvationEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getRMSGradient(), 31.6410816)
Size i = 0;
Vector3 force;
AtomIterator atom_it = s.beginAtom();
for (; +atom_it; ++atom_it, ++i)
{
switch (i)
{
// values are taken from CHARMM calculaction
// (version 27b1 with param19_eef1.inp and toph19_eef1.inp,
// with modified nonbonded: atom rdiel cutnb 20. cutonnb 11. cutofnb 15.)
case 0: force = Vector3( 0.00000, 0.00000, 0.00000); break;
case 1: force = Vector3( 0.00000, 0.00000, 0.00000); break;
case 2: force = Vector3( 0.00000, 0.00000, 0.00000); break;
case 3: force = Vector3( 0.00000, 0.00000, 0.00000); break;
case 4: force = Vector3( 4.98047, 2.50327, -6.64754); break;
case 5: force = Vector3(-16.96076, -8.20699, 25.84288); break;
case 6: force = Vector3( 5.27421, 2.34230, -10.15213); break;
case 7: force = Vector3( 6.70608, 3.36142, -9.04320);
}
force = force - atom_it->getForce() * Constants::NA * 1e-13 / -4.184;
TEST_REAL_EQUAL(force.getLength(), 0.0)
}
RESULT
CHECK(force test 5 (GLY, VdW only) [EEF1])
// read the PDB file containing a single GLY
PDBFile f(BALL_TEST_DATA_PATH(CharmmFF_test_1.pdb));
System s;
f >> s;
f.close();
// check whether we got the right number of atoms
TEST_EQUAL(s.countAtoms(), 8)
// normalize the names and build the bonds
s.apply(frag_db.normalize_names);
s.apply(frag_db.build_bonds);
CharmmFF eef1;
// remove all components excecpt for VdW
eef1.removeComponent("CHARMM Torsion");
eef1.removeComponent("CHARMM ImproperTorsion");
eef1.removeComponent("CHARMM Bend");
eef1.removeComponent("CHARMM Stretch");
eef1.options[CharmmFF::Option::USE_EEF1] = "false";
eef1.options[CharmmFF::Option::ASSIGN_CHARGES] = "true";
eef1.options[CharmmFF::Option::ASSIGN_TYPENAMES] = "true";
eef1.options[CharmmFF::Option::ASSIGN_TYPES] = "true";
eef1.options[CharmmFF::Option::FILENAME] = "CHARMM/EEF1/param19_eef1.ini";
eef1.setup(s);
ClearChargeProcessor clear_charges;
s.apply(clear_charges);
eef1.updateForces();
eef1.updateEnergy();
TEST_REAL_EQUAL(eef1.getEnergy(), 26.64563664)
TEST_REAL_EQUAL(eef1.getBendEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getProperTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getImproperTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getStretchEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getESEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getVdWEnergy(), 26.64563664)
TEST_REAL_EQUAL(eef1.getSolvationEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getRMSGradient(), 59.16799416)
Size i = 0;
Vector3 force;
AtomIterator atom_it = s.beginAtom();
for (; +atom_it; ++atom_it, ++i)
{
switch (i)
{
// values are taken from CHARMM calculaction
// (version 27b1 with param19_eef1.inp and toph19_eef1.inp,
// with modified nonbonded: atom rdiel cutnb 20. cutonnb 11. cutofnb 15.)
case 0: force = Vector3(-29.88574, 42.58230, -9.95883); break;
case 1: force = Vector3( 0.00347, -0.15351, 0.08606); break;
case 2: force = Vector3( 0.12799, 5.71407, -0.44357); break;
case 3: force = Vector3( 0.11338, -0.22339, 0.06770); break;
case 4: force = Vector3( 0.00000, 0.00000, 0.00000); break;
case 5: force = Vector3( 25.47118, -20.67960, 10.22273); break;
case 6: force = Vector3( 4.45634, -27.56737, 0.20325); break;
case 7: force = Vector3( -0.28662, 0.32750, -0.17734);
}
force = force - atom_it->getForce() * Constants::NA * 1e-13 / -4.184;
TEST_REAL_EQUAL(force.getLength(), 0.0)
}
RESULT
CHECK(force test 6 (2 atoms, electrostatic only) [EEF1/CDIEL])
// read the PDB file containing a single GLY
PDBFile f(BALL_TEST_DATA_PATH(CharmmFF_test_2.pdb));
System s;
f >> s;
f.close();
// check whether we got the right number of atoms
TEST_EQUAL(s.countAtoms(), 2)
// normalize the names and build the bonds
s.apply(frag_db.normalize_names);
CharmmFF eef1;
// remove all components excecpt for electrostatics
eef1.removeComponent("CHARMM Torsion");
eef1.removeComponent("CHARMM ImproperTorsion");
eef1.removeComponent("CHARMM Bend");
eef1.removeComponent("CHARMM Stretch");
eef1.options[CharmmFF::Option::USE_EEF1] = "false";
eef1.options[CharmmFF::Option::ASSIGN_CHARGES] = "true";
eef1.options[CharmmFF::Option::ASSIGN_TYPENAMES] = "true";
eef1.options[CharmmFF::Option::ASSIGN_TYPES] = "true";
eef1.options[CharmmFF::Option::DISTANCE_DEPENDENT_DIELECTRIC] = "false";
eef1.options[CharmmFF::Option::FILENAME] = "CHARMM/EEF1/param19_eef1.ini";
// turn off vdW interactions
eef1.options[CharmmFF::Option::VDW_CUTOFF] = 0.1;
eef1.options[CharmmFF::Option::VDW_CUTON] = 0.05;
eef1.setup(s);
eef1.updateForces();
eef1.updateEnergy();
TEST_REAL_EQUAL(eef1.getEnergy(), -910.321)
TEST_REAL_EQUAL(eef1.getBendEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getProperTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getImproperTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getStretchEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getESEnergy(), -910.321)
TEST_REAL_EQUAL(eef1.getVdWEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getSolvationEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getRMSGradient(), 212.569)
Size i = 0;
Vector3 force;
AtomIterator atom_it = s.beginAtom();
for (; +atom_it; ++atom_it, ++i)
{
force = atom_it->getForce() * Constants::NA * 1e-13;
TEST_REAL_EQUAL(force.getLength(), 368.181)
}
RESULT
CHECK(force test 7 (2 atoms, electrostatic only) [EEF1/RDIEL])
// read the PDB file containing a single GLY
PDBFile f(BALL_TEST_DATA_PATH(CharmmFF_test_2.pdb));
System s;
f >> s;
f.close();
// check whether we got the right number of atoms
TEST_EQUAL(s.countAtoms(), 2)
// normalize the names and build the bonds
s.apply(frag_db.normalize_names);
CharmmFF eef1;
// remove all components excecpt for electrostatics
eef1.removeComponent("CHARMM Torsion");
eef1.removeComponent("CHARMM ImproperTorsion");
eef1.removeComponent("CHARMM Bend");
eef1.removeComponent("CHARMM Stretch");
eef1.options[CharmmFF::Option::USE_EEF1] = "false";
eef1.options[CharmmFF::Option::ASSIGN_CHARGES] = "true";
eef1.options[CharmmFF::Option::ASSIGN_TYPENAMES] = "true";
eef1.options[CharmmFF::Option::ASSIGN_TYPES] = "true";
eef1.options[CharmmFF::Option::FILENAME] = "CHARMM/EEF1/param19_eef1.ini";
// turn off vdW interactions
eef1.options[CharmmFF::Option::VDW_CUTOFF] = 0.1;
eef1.options[CharmmFF::Option::VDW_CUTON] = 0.05;
eef1.options[CharmmFF::Option::DISTANCE_DEPENDENT_DIELECTRIC] = "true";
eef1.setup(s);
eef1.updateForces();
eef1.updateEnergy();
TEST_REAL_EQUAL(eef1.getEnergy(), -368.181)
TEST_REAL_EQUAL(eef1.getBendEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getProperTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getImproperTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getTorsionEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getStretchEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getESEnergy(), -368.181)
TEST_REAL_EQUAL(eef1.getVdWEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getSolvationEnergy(), 0.0)
TEST_REAL_EQUAL(eef1.getRMSGradient(), 171.948)
Size i = 0;
Vector3 force, a1, a2;
AtomIterator atom_it = s.beginAtom();
for (; +atom_it; ++atom_it, ++i)
{
force = atom_it->getForce() * Constants::NA * 1e-13;
TEST_REAL_EQUAL(force.getLength(), 297.823)
}
RESULT
CHECK(force test 8 (2 atoms, ES switching function) [EEF1/RDIEL])
// read the PDB file containing two atoms
PDBFile f(BALL_TEST_DATA_PATH(CharmmFF_test_2.pdb));
System s;
f >> s;
f.close();
// check whether we got the right number of atoms
TEST_EQUAL(s.countAtoms(), 2)
// normalize the names and build the bonds
s.apply(frag_db.normalize_names);
CharmmFF eef1;
// remove all components excecpt for electrostatics
eef1.removeComponent("CHARMM Torsion");
eef1.removeComponent("CHARMM ImproperTorsion");
eef1.removeComponent("CHARMM Bend");
eef1.removeComponent("CHARMM Stretch");
eef1.options[CharmmFF::Option::USE_EEF1] = "false";
eef1.options[CharmmFF::Option::ASSIGN_CHARGES] = "true";
eef1.options[CharmmFF::Option::ASSIGN_TYPENAMES] = "true";
eef1.options[CharmmFF::Option::ASSIGN_TYPES] = "true";
eef1.options[CharmmFF::Option::FILENAME] = "CHARMM/EEF1/param19_eef1.ini";
// turn off vdW interactions
eef1.options[CharmmFF::Option::VDW_CUTOFF] = 0.1;
eef1.options[CharmmFF::Option::VDW_CUTON] = 0.05;
eef1.options[CharmmFF::Option::ELECTROSTATIC_CUTON] = 2.0;
eef1.options[CharmmFF::Option::ELECTROSTATIC_CUTOFF] = 4.0;
eef1.options[CharmmFF::Option::DISTANCE_DEPENDENT_DIELECTRIC] = "true";
eef1.setup(s);
Size i = 0;
Vector3 force;
Atom* a1;
Atom* a2;
AtomIterator atom_it = s.beginAtom();
for (; +atom_it; ++atom_it, ++i)
{
switch (i)
{
case 0: a1 = &*atom_it; break;
case 1: a2 = &*atom_it; break;
}
}
TEST_NOT_EQUAL(a1, 0)
TEST_NOT_EQUAL(a2, 0)
// set one atom to the origin
a1->setPosition(Vector3(0.0));
i = 0;
for (double d = 1.2; d < 6.0; d += 0.2, i++)
{
a2->setPosition(Vector3(d, 0.0, 0.0));
eef1.updateForces();
double energy = eef1.updateEnergy();
double force = a1->getForce().x * Constants::NA / 1e13;
switch (i)
{
case 0:
TEST_REAL_EQUAL(force, 2605.04)
TEST_REAL_EQUAL(energy, -1563.02)
break;
case 1:
TEST_REAL_EQUAL(force, 1640.49)
TEST_REAL_EQUAL(energy, -1148.34)
break;
case 2:
TEST_REAL_EQUAL(force, 1099)
TEST_REAL_EQUAL(energy, -879.201)
break;
case 3:
TEST_REAL_EQUAL(force, 771.864)
TEST_REAL_EQUAL(energy, -694.677)
break;
case 4:
TEST_REAL_EQUAL(force, 562.688)
TEST_REAL_EQUAL(energy, -562.688)
break;
case 5:
TEST_REAL_EQUAL(force, 483.433)
TEST_REAL_EQUAL(energy, -458.515)
break;
case 6:
TEST_REAL_EQUAL(force, 424.043)
TEST_REAL_EQUAL(energy, -368.004)
break;
case 7:
TEST_REAL_EQUAL(force, 375.014)
TEST_REAL_EQUAL(energy, -288.214)
break;
case 8:
TEST_REAL_EQUAL(force, 330.421)
TEST_REAL_EQUAL(energy, -217.707)
break;
case 9:
TEST_REAL_EQUAL(force, 286.361)
TEST_REAL_EQUAL(energy, -156.013)
break;
case 10:
TEST_REAL_EQUAL(force, 240.127)
TEST_REAL_EQUAL(energy, -103.309)
break;
case 11:
TEST_REAL_EQUAL(force, 189.744)
TEST_REAL_EQUAL(energy, -60.2396)
break;
case 12:
TEST_REAL_EQUAL(force, 133.7)
TEST_REAL_EQUAL(energy, -27.7899)
break;
case 13:
TEST_REAL_EQUAL(force, 70.7883)
TEST_REAL_EQUAL(energy, -7.21769)
break;
default: // above cutoff -> everything equals zero
TEST_REAL_EQUAL(force, 0.0)
TEST_REAL_EQUAL(energy, 0.0)
}
}
RESULT
/////////////////////////////////////////////////////////////
/////////////////////////////////////////////////////////////
END_TEST
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