| 2:23:52 PM PDT - Thu, Sep 5th 2013 |
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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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