What is the atom index in Metadynamic block
Clicked A Few Times
11:20:16 PM PST - Sun, Feb 16th 2014
Dear all,
I want to perform the metadynamic simulation and not sure how to determine the atom_index in medadynamic input block.
According to the manual (e.g. bond as a collective variable):

BOND <integer atom1_index no default> <integer atom2_index no default>

I want to know what is the atom_index in Metadynamic block.
Does it correspond to the atomic order given in Geometry block?
for example:
geometry units au 
  O      0.00000000    0.00000000    0.00000000     atom_index  1?

  H      0.00000000    1.43042809   -1.10715266     atom_index  2?

  H      0.00000000   -1.43042809   -1.10715266     atom_index  3?

end
Any help will be appreciated.
Youzhao Lan

Clicked A Few Times
6:34:50 PM PST - Mon, Feb 17th 2014
From nwchem mail-list:

Hi Youzhao,
Indeed as you guessed the atom_index is simply the number of the atom in the list of atoms in the geometry. So the example you constructed:
geometry units au
O 0.00000000 0.00000000 0.00000000 atom_index 1
H 0.00000000 1.43042809 -1.10715266 atom_index 2
H 0.00000000 -1.43042809 -1.10715266 atom_index 3
end
is correct.
Best wishes,
   Huub


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