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geoopt
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All input and output files can be downloaded here.

Geometry Optimization

Geometry optimization intends to find a minimum on the potential energy surface from a starting geometry. All energy calculation methods, including quantum mechanics (QM), molecular mechanics (MM), and QM/MM, can be used for geometry optimization, as long as you change energy to opt in the input files.

Three Optimizations

QM Geometry Optimization

For water in Density Functional Theory Calculations, the geometry optimization is:

basis
    def2-tzvp
end

scf
    charge  0
    spin2p1 1
    type    R
end

grimmedisp
    type bj
end

mol
   O  0.    0.00000000   -0.11081188
   H  0.   -0.78397589    0.44324751
   H  0.    0.78397589    0.44324751
end

task
    opt b3lyp # Just change energy to opt.
end

After optimization, you will find two additional files:

  • water-opt.xyz The last optimized structure. It is updating during the optimization.
  • water-opt-traj.xyz All intermediate structures during the optimization.

MM Geometry Optimization

The protein example in Molecular Mechanics Energy can be easily changed for geometry optimization:

charmm
    parameters par_all36m_prot.prm toppar_water_ions.str
    topology   step2_solvator.psf
    scaling14  1.0
    rcutoff    12.0
    rswitch    10.0
    use_PBC
    Lbox 64 64 64
    electrostatic pme
    PMEk   64 64 64
end

mol
    step2_solvator.pdb
end

task
    opt charmm
end

QM/MM Geometry Optimization

Both examples in Quantum Mechanics/Molecular Mechanics (QM/MM) Energy can be easily changed for geometry optimization, as long as you change energy to opt. For example:

charmm
    parameters par_all36m_prot.prm
    topology   step1_pdbreader.psf
    scaling14  1.0
    rcutoff    12.0
    rswitch    13.0
end

basis
    def2-svp
end

scf
    charge  0
    spin2p1 1
    type    R
end

grimmedisp
    type bj
end

qmmm
    qm_region  779 792-815
end

mol
    step1_pdbreader.pdb
end

task
    opt b3lyp/charmm
end

Some Options

There are some options for geometry optimization. For example, the following example:

basis
    def2-svp
end

scf
    charge  0
    spin2p1 1
    type    R
end

grimmedisp
    type bj
end

opt
   num_steps   1000
   epsilon     1.E-5
   fix         1-9
end

mol
      C                 -4.08368628    0.86864405    0.00000000
      H                 -3.72701344    1.37304224   -0.87365150
      H                 -5.15368628    0.86865724    0.00000000
      C                 -3.57037057   -0.58328810    0.00000000
      H                 -3.92704565   -1.08768708   -0.87365013
      H                 -3.92704123   -1.08768606    0.87365253
      C                 -2.03037057   -0.58330630   -0.00000339
      H                 -1.67371614   -1.59211630   -0.00000091
      H                 -1.67370018   -0.07891023   -0.87365712
      O                 -3.60701136    1.54274631    1.16759033
      H                 -4.11695915    2.34433532    1.30546096
      O                 -1.55369311    0.09080013    1.16758349
      H                 -2.04104440   -0.21550578    1.93587082
end

task
    opt b3lyp
end

The geometry optimization control block is opt ... end:

  • num_steps The maximum number of geometry steps. Default is 1000.
  • epsilon A convergence label. Usually, you do not need to change it.
  • fix The atoms that you want to fix during geometry optimization.

In the above example, we fix the alkyl chain and only relax the hydroxyl groups. The final optimization result can be seen in c3h8o2-opt.xyz and c3h8o2-opt-traj.xyz. The animation of the optimization is shown below. Obviously, atoms 1-9 have been fixed.

image