modified on 11 September 2014 at 15:03 ••• 1,031 views

Release66:Qmmm optimization analysis

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Analysis of QM/MM optimization

The progress of QM/MM optimization can be tracked from the output file by doing search for "@"

grep @ *.out

or "@ total"

grep "@ total" *out

In the first case all the individual optimization steps will be displayed (which could be overwhelming for large optimization jobs). More terse output will be obtained in the second case, where only total qmmm energy for each optimization pass will be displayed, e.g.

marat-macbook:example-7 >grep "@ total" example-7.nwout                                                                                                       (Wed 4:12pm )
@ total qmmm energy                   -93.098719031 (-.244431E+06  kjoule/mol)
@ total qmmm energy                   -93.140883369 (-.244541E+06  kjoule/mol)
@ total qmmm energy                   -93.142258541 (-.244545E+06  kjoule/mol)
@ total qmmm energy                   -93.159553191 (-.244590E+06  kjoule/mol)
@ total qmmm energy                   -93.159855467 (-.244591E+06  kjoule/mol)
marat-macbook:example-7 >                                                                                                                                                     (Wed 4:12pm )


If the xyz option was specified the structures of corresponding region during the optimization may be visualized through the xyz files. In addition, at the end of each optimization pass, a restart file named system.NNN.rst is written to the permanent directory (here NNN stands for current optimization cycle counter). So for example in the case of this input file one will end up with wtr.001.rst, wtr.002.rst, ..., wtr.005.rst files. These restart files can be used to continue aborted calculation, and also for the generation of the pdb file for the entire system using the following input file:


  # Given topology wtr.top and
  # restart file wtr_ref.rst
  # pdb file can be generated
  start wtr
  prepare
  read wtr_ref.rst
  write wtr_ref.pdb
  end
  task prepare