modified on 11 September 2014 at 15:03 ••• 1,750 views

Release66:QMMM Parameters

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Template:Release66:QMMM Input Links The QM/MM interface parameters define the interaction between classical and quantum regions.

 qmmm
 [ eref <double precision default 0.0d0>]
 [ bqzone <double precision default 9.0d0>]
 [ mm_charges [exclude <(none||all||linkbond||linkbond_H) default none>]
          [ expand  <none||all||solute||solvent> default none]
          [ update  <integer default 0>] 
 [ link_atoms <(hydrogen||halogen) default hydrogen>]
 [ link_ecp  <(auto||user) default auto>]
 [ region   < [region1]  [region2]  [region3] > ]
 [ method   [method1]  [method2]  [method3]  ]
 [ maxiter  [maxiter1] [maxiter2] [maxiter3] ]
 [ ncycles  < [number] default 1 > ]
 [ density  [espfit] [static] [dynamical] ]
 [ xyz  ]
 [ convergence <double precision default 1.0d-4>] ]
 [ rename ] <filename>
 [ nsamples ]
 end


Detailed explanation of the subdirectives in the QM/MM input block is given below:


eref <double precision default 0.0d0>

This directive sets the relative zero of energy for the QM component of the system. The need for this directive arises from different definitions of zero energy for QM and MM methods. In QM methods the zero of energy for the system is typically vacuum. The zero of energy for the MM system is by definition of most parameterized force fields the separated atom energy. Therefore in many cases the energetics of the QM system will likely overshadow the MM component of the system. This imbalance can be corrected by suitably chosen value of eref. In most cases IT IS OK to leave eref at its default value of zero.


bqzone <double precision default 9.0d0>

This directive defines the radius of the zone (in angstroms) around the quantum region where classical residues/segments will be allowed to interact with quantum region both electrostatically and through Van der Waals interactions. It should be noted that classical atoms interacting with quantum region via bonded interactions are always included (this is true even if bqzone is set to 0). In addition, even if one atom of a given charged group is in the bqzone (residues are typically treated as one charged group) then the whole group will be included.


mm_charges [exclude <(none||all||linkbond||linkbond_H) default none>]
           [expand  <none||all||solute||solvent> default none]
           [update  <integer default 0>]

This directive controls treatment of classical point (MM) charges that are interacting with QM region. For most QM/MM applications the use of directive will be not be necessary. Its absence would be simply mean that all MM charges within the cuttof distance ( as specified by cutoff ) as well those belonging to the charges groups directly bonded to QM region will be allowed to interact with QM region.

Keyword exclude specifies the subset MM charges that will be specifically excluded from interacting with QM region.

  • none default value reverts to the original set of MM charges as described above.
  • all excludes all MM charges from interacting with QM region ("gas phase" calculation).
  • linkbond excludes MM charges that are connected to a quantum region by at most two bonds,
  • linkbond_H similar to linkbond but excludes only hydrogen atoms.

Keyword expand expands the set MM charges interacting with QM region beyond the limits imposed by cutoff value.

  • none default value reverts to the original set of MM charges
  • solute expands electrostatic interaction to all solute MM charges
  • solvent expands electrostatic interaction to all solvent MM charges
  • all expands electrostatic interaction to all MM charges

Keyword update specifies how often list of MM charges will be updated in the course of the calculation. Default behavior is not to update.


link_atoms <(hydrogen||halogen) default halogen>

This directive controls the treatment of bonds crossing the boundary between quantum and classical regions. The use of hydrogen keyword will trigger truncation of such bonds with hydrogen link atoms. The position of the hydrogen atom will be calculated from the coordinates of the quantum and classical atom of the truncated bond using the following expression

\mathbf{R}_{hlink} = (1-g)\mathbf{R}_{quant} + g*\mathbf{R}_{class}

where g is the scale factor set at 0.709

Setting link_atoms to halogen will result in the modification of the quantum atom of the truncated bond to to the fluoride atom. This fluoride atom will typically carry an effective core potential (ECP) basis set as specified in link_ecp directive.


link_ecp  <(auto||user) default auto>

This directive specifies ECP basis set on fluoride link atoms. If set to auto the ECP basis set given by Zhang, Lee, Yang for 6-31G* basis.35.2 will be used. Strictly speaking, this implies the use of 6-31G* spherical basis as the main basis set. If other choices are desired then keyword user should be used and ECP basis set should be entered separatelly following the format given in section 8. The name tag for fluoride link atoms is F_L.


region  < [region1]  [region2]  [region3] >

This directive specifies active region(s) for optimization, dynamics, frequency, and free energy calculations. Up to three regions can be specified, those are limited to

  • "qm" - all quantum atoms some text
  • "qmlink" - quantum and link atoms
  • "mm_solute" - all classical solute atoms excluding link atoms
  • "solute" - all solute atoms including quantum
  • "solvent" all solvent atoms
  • "mm" all classical solute and solvent atoms, excluding link atoms
  • "all" all atoms

Only the first region will be used in dynamics, frequency, and free energy calculations. In the geometry optimizations, all three regions will be optimized using the following optimization methods

    if (region.eq."qm") then
       method = "bfgs"
     else if (region.eq."qmlink") then
       method = "bfgs"
     else if (region.eq."mm_solute") then
       method = "lbfgs"
     else if (region.eq."mm") then
       method = "sd"
     else if (region.eq."solute") then
       method = "sd"
     else if (region.eq."solvent") then
       method = "sd"
     else if (region.eq."all") then
       method = "sd"
     end if

where "bfgs" stands for Broyden–Fletcher–Goldfarb–Shanno (BFGS) optimization method, "lbfgs" limited memory version of quasi-newton, and "sd" simple steepest descent algorithm. These assignments can be potentially altered using method directive.


method   [method1]  [method2]  [method3]

This directive controls which optimization algorithm will be used for the regions as defined by regions directive. The allowed values are "bfgs" aka driver, "lbfgs" limited memory version of quasi-newton, and "sd" simple steepest descent algorithm. The use of this directive is not recommended in all but special cases. In particular, "bfgs" should be used for QM region if there are any constraints, "sd" method should always be used for classical solute and solvent atoms with shake constraints.

Release66:Qmmm maxiter


ncycles  < [number] default 1 >

This directive controls the number of optimization cycles where the defined regions will be optimized in succession, or number of sampling cycles in free energy calculations.


density  [espfit] [static] [dynamical] default dynamical

This directive controls the electrostatic representation of fixed QM region during optimization/dynamics of classical regions. It has no effect when position of QM atoms are changing.

  • dynamical is an option where QM region is treated the standard way, through the recalculation of the wavefunction calculated and the resulting electron density is used to compute electrostatic interactions with classical atoms. This option is the most expensive one and becomes impractical for large scale optimizations.
  • static option will not recalculate QM wavefunction but will still use full electron density in the computations of electrostatic interactions.
  • espfit option will not recalculate QM wavefunction nor it will use full electron density. Instead, a set of ESP charges for QM region will be calculated and used to compute electrostatic interactions with the MM regions. This option is the most efficient and is strongly recommended for large systems.

Note that both "static" and "espfit" options do require the presence of the movecs file. It is typically available as part as part of calculation process. Otherwise it can be generated by running qmmm energy calculation.

In most calculations default value for density would dynamical, with the exception of free energy calculations where default setting espfit will be used.


rename <filename>

This directive is allows to rename atoms in the QM region, based on the external file which specifies desired name( (1st column) and its PDB index (2nd column). The file is assumed to be located in the current run directory.

For example, if we need to rename atoms CB and OG that are part of our QM region

 ...
 ATOM     13  N   SER     2       0.211   0.284  -1.377        0.00     N
 ATOM     14  H   SER     2       0.886   1.158  -1.257        0.00     H
 ATOM     15  CA  SER     2      -0.320  -0.351  -0.166        0.00     C
 ATOM     16  HA  SER     2      -1.405  -0.183  -0.132        0.00     H
 ATOM     17  CB  SER     2      -0.001  -1.879  -0.106        0.00     C
 ATOM     18 2HB  SER     2       1.092  -2.012  -0.038        0.00     H
 ATOM     19 3HB  SER     2      -0.469  -2.317   0.784        0.00     H
 ATOM     20  OG  SER     2      -0.452  -2.678  -1.192        0.00     O
 ATOM     21  HG  SER     2      -1.351  -2.421  -1.392        0.00     H
 ATOM     22  C   SER     2       0.252   0.338   1.076        0.00     C
 ...

the following qmmm block can be used

 ...
 qmmm
  ...
  rename name.dat
  ...
 end
 
 task qmmm dft energy


where name.dat file

C1 17
OX 20

Here atoms are identified by the corresponding PDB atom index and renamed from default element based naming to C1 and OX.


convergence  < double precision etol default 1.0d-4>

This directive controls convergence of geometry optimization. The optimization is deemed converged if absolute difference in total energies between consecutive optimization cycles becomes less than etol.


nsamples 

This directive is required for free energy calculations and defines number of samples for averaging during single cycle.