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Example: Learning Atom-based Parameters from an Ensemble of Structures
The learn statement is used to derive equilibrium geometries and energy constants simultaneously from a thermal ensemble of ten coordinate files:
{*Only the active energy terms are affected by the learn statement.*}
flags exclude * include bonds angles dihedrals impropers end
{*Initiate the learning process.*}
parameters
learn initiate sele=(all) mode=statistics end
end
{*Loop through the ensemble of coordinates.*}
for $filename in ( "a1.pdb" "a2.pdb" "a3.pdb" "a4.pdb" "a5.pdb"
"a6.pdb" "a7.pdb" "a8.pdb" "a9.pdb" "a10.pdb" )
loop main
coordinates @@$filename
parameters
learn accumulate end
end
end loop main
{*Now we terminate the learning process.*}
parameters
learn terminate end
end
{*One could now compute energies with the learned parameters or *}
{*reduce them to type-based parameters and write them to a file.*}
Instead of learning from an ensemble of coordinates, one could have also learned the coordinates from a trajectory (Section 12.2).
Xplor-NIH 2024-09-13