PSPW QM/MM: Different types of MM atoms of the same element

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2:23:52 PM PDT - Thu, Sep 5th 2013
As per an e-mail response by Eric Bylaska:

You just add a 1 or 2 character label after the "^"

Here's an example where I specified two different oxygens.  In addition to the LJ parameters, you'll also need include an mm_psp command to generate a psp potential for the "O^1" MM atom.

Eric

title "CCl4 + 3water64"

start CCl4-water3

scratch_dir   ./perm
permanent_dir ./perm


charge 0

geometry units angstrom nocenter noautosym noautoz print xyz
C        0.7929E-02 -0.2760E-02  0.1903E-02
Cl      -0.8602E+00  0.1547E+01  0.2561E+00
Cl       0.8423E+00 -0.4773E+00  0.1519E+01
Cl      -0.1167E+01 -0.1279E+01 -0.4588E+00
Cl       0.1218E+01  0.1974E+00 -0.1309E+01

O^1       0.3253E+01 -0.4435E+01 -0.5947E+01 -0.2397E-04 -0.1467E-03 -0.7805E-05
H^       0.3215E+01 -0.4846E+01 -0.5036E+01 -0.6720E-04 -0.1204E-04  0.7077E-04
H^       0.4195E+01 -0.4458E+01 -0.6283E+01  0.4576E-04 -0.1418E-03  0.8799E-04
O^       0.5344E+01 -0.3346E+01 -0.1214E+01 -0.3312E-04 -0.8827E-04  0.1682E-04
H^       0.5001E+01 -0.3063E+01 -0.2109E+01  0.2729E-03 -0.1219E-03 -0.1323E-03
H^       0.5678E+01 -0.2546E+01 -0.7162E+00 -0.8406E-04 -0.5326E-04 -0.4349E-05
O^       0.3991E+01 -0.1538E+01  0.1664E+01 -0.3050E-04 -0.1426E-03 -0.1117E-04
H^       0.4084E+01 -0.2240E+01  0.2370E+01 -0.7053E-04 -0.1202E-03  0.6620E-04
H^       0.4880E+01 -0.1110E+01  0.1501E+01  0.8933E-05 -0.1389E-03  0.5445E-04
end
set nwpw:cif_filename ccl4water


NWPW
   QMMM

      mm_psp O^1 -0.8476 4 0.70

      lj_ion_parameters C  3.41000000d0 0.10000000d0
      lj_ion_parameters Cl  3.45000000d0 0.16d0
      lj_ion_parameters O^ 3.16555789d0 0.15539425d0
      lj_ion_parameters O^1 3.26555789d0 0.15539425d0

      # new input format
      fragment spc
         size 3
         index_start 6:12:3

         #shake units angstroms 1 2 3 cyclic 1.0 1.632993125 1.0
         bond_spring 1 2    0.467307856 1.889726878
         bond_spring 1 3    0.467307856 1.889726878
         angle_spring 2 1 3 0.07293966  1.910611932

      end

   END
END


            • Setup conjugate gradient code ****
nwpw
   SIMULATION_CELL
      #boundary_conditions aperiodic
      SC 14.00
      ngrid   16 16 16
   END
   lmbfgs
   mapping 2
   translation on
   np_dimensions 1 2
   tolerances 1.0e-11 1.0e-11
end
task pspw energy
task pspw gradient

set geometry:actlist 6:197


nwpw
   car-parrinello
      #Nose-Hoover 1410.0 300.0 1410.0 300.0 clear
      initial_ion_temperature none
      time_step 5.00
      fake_mass 750.0
      loop 2 2
    end
end
task pspw car-parrinello
task pspw noit_energy


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