modified on 18 February 2011 at 13:50 ••• 66,161 views

Qmmm Setup

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QM/MM Restart and Topology files: Prerequisites | QM region definition | Solvation | Permanent Constraints

The structure of the system in QM/MM calculations is provided by the restart file (extension .rst) and not by the geometry block as it would be for pure QM calculations. The parameters of classical interaction are given by the topology file (extension .top). These two files are REQUIRED for QM/MM calculations and can be generated by the prepare module. In a typical setting this "preparation stage" is performed separately from the main QM/MM simulation.

Basic Structure of QM/MM input file

The input file for QM/MM calculations contains definition of molecular mechanics parameters, quantum mechanical parameters, and QM/MM interface parameters.

Molecular Mechanics (MM) parameters

The molecular mechanics parameters are given in the form of standard MD input block as used by the MD module. At the basic level the molecular mechanics input block specifies the restart and topology file that were generated during QM/MM preparation stage. It also contains information relevant to the calculation of the classical region (e.g. cutoff distances, constraints, optimization and dynamics parameters, etc) in the system. In this input block one can also set fixed atom constraints on classical atoms. Continuing with our example for ethanol molecule here is a simple input block that may be used for this system.

# this specifies that etl_md.rst will be used as a restart file
#  and will be a topology file
  system etl_md
# if we ever wanted to fix C1 atom 
  fix solute 1 _C1
  noshake solute

The noshake solute, shown in the above example is a recommended directive for QM/MM simulations that involve optimizations. Otherwise user has to ensure that the optimization method for classical solute atoms is a steepest descent

Quantum Mechanics (QM) parameters

The QM/MM interface parameters define the interaction between classical and quantum regions. Depending on the nature of the calculation there are number of parameters that can be defined The parameters defining calculation of the QM region (including basis sets) must be present in the traditional NWChem input format except for the geometry block. The geometrical information will be constructed automatically using information contained in the restart file.

QM/MM Interface parameters

The QM/MM interface parameters define the interaction between classical and quantum regions. These include definition of the link atoms used in the truncating the bonds connecting QM and MM regions (link_atoms and link_ecp), details of the long-range interactions between QM and MM regions (mm_charges and bqzone), and other parameters applicable for specific types of QM/MM tasks. These setting will be discussed in details in the latter sections.

 [ 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] default dynamical ]
 [ xyz  ]
 [ convergence <double precision default 1.0d-4>] ]
 [ load ]