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
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