Working with force fields

Preparation

Force fields in BiochemicalAlgorithms.jl are always set up for a given molecular system. Hence, we first need to prepare a System object as usual, e.g., by loading a structure from a PDB file and applying our fragment database preprocessors:

sys = load_pdb(ball_data_path("../test/data/AlaAla.pdb"))

fdb = FragmentDB()
normalize_names!(sys, fdb)
reconstruct_fragments!(sys, fdb)
build_bonds!(sys, fdb)

sys

[ Info: reconstruct_fragments!(): added 0 atoms.
[ Info: build_bonds!(): built 22 bonds

System{Float32}: AlaAla.pdb
  23 atoms
  22 bonds
   1 molecules
   1 chains
   0 secondary structures
   2 fragments

Setting up a force field

Setting up a force field boils down to a simple constructor call:

ff = AmberFF(sys)

┌ Warning: 2 warnings occurred during setup that were suppressed:
│  - Torsion: 2 warnings
│ Use print_warnings(ff) to display them.
└ @ BiochemicalAlgorithms ~/git/ball.jl/src/forcefields/common/forcefield.jl:233

AmberFF for 23 atoms with 22 bonds.

This will initialize the force field object using the atoms (and their positions in particular) as seen at time of construction. Later alterations of the same system must be made known to the force field by calling the update! function:

update!(ff)

Force computation

Force vectors for all atoms can be computed using the compute_forces! function:

compute_forces!(ff)

The force vectors computed here are directly stored in the underlying system:

atoms(sys).F   # or, equivalently, atoms(ff.system).F

23-element SystemComponentTableCol{StaticArraysCore.SVector{3, Float32}}:
 [-8.9053415f-10, -3.7217035f-10, 4.139505f-10]
 [7.8021095f-10, 5.121153f-11, -4.5226357f-11]
 [2.1271644f-9, 7.604931f-10, -1.7229931f-9]
 [6.35672f-8, 4.1203474f-8, -1.4751437f-7]
 [-6.499216f-11, -9.3102845f-11, 5.374651f-11]
 [4.2136683f-11, -7.511121f-11, 1.08262434f-10]
 [8.747169f-12, -6.845735f-11, 8.273652f-11]
 [6.9892536f-11, 1.4578987f-11, -3.084564f-11]
 [-1.9595295f-10, -1.1358163f-10, -1.1052923f-10]
 [7.265452f-11, 4.82974f-11, -4.4509858f-11]
 ⋮
 [2.466124f-10, -1.1778086f-9, 2.6044453f-9]
 [8.27785f-10, -5.424906f-10, 8.765798f-10]
 [3.351959f-11, -1.4663636f-10, 3.1680897f-11]
 [4.1687837f-11, 5.738371f-12, 1.0522515f-10]
 [7.105667f-11, -7.694347f-11, 1.3604341f-10]
 [-4.5483453f-10, 7.660909f-10, -6.81682f-10]
 [9.818543f-12, -2.6953412f-10, 2.1820956f-10]
 [-6.470714f-8, -4.2964025f-8, 1.4709109f-7]
 [-2.1067495f-10, 1.2029508f-10, -2.3378374f-10]

Potential energy computation

Similarly, potential energies can be computed via compute_energy!:

compute_energy!(ff)

1425.6062f0

This will return the total energy of the system (in kJ/mol). Additionally, the force field object keeps track of individual contributions of force field components, which can be queried like this:

ff.energy

Dict{String, Float32} with 7 entries:
  "Angle Bends"      => 5.40767
  "Hydrogen Bonds"   => 0.0
  "Bond Stretches"   => 1.36306
  "Van der Waals"    => 1493.18
  "Improper Torsion" => 3.99017f-6
  "Electrostatic"    => -85.1467
  "Proper Torsion"   => 10.7981

Structure optimization

The force field object can also be used to find a structure minimizing the total energy of the system:

optimize_structure!(ff)
compute_energy!(ff)

-374.3145f0

The opmitization function also updates the atom positions correspondingly such that the structure can be visualized in its optimized state, e.g., through BiochemicalVisualization.jl.

We provide a variant of the optimization function above to only optimize the positions of hydrogen atoms:

optimize_hydrogen_positions!(ff)