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Martin Kurečka
Plumed AlphaFold
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bb0418ce
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bb0418ce
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Giovanni Bussi
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clarified neighbor list explanation
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@@ -127,6 +127,16 @@ Collective variables that can be speed up making us of neighbour lists:
By tuning the cut-off for the neighbour list and the frequency for the recalculation of the list it is
possible to balance between accuracy and performances.
Notice that for \ref COORDINATION and \ref DHENERGY using a neighbor list could imply that a smaller
number of atoms are requested to the host MD engine. This is typically true when considering
\ref COORDINATION of a small number of atoms (e.g. a ligand) again many atoms (e.g. water).
When the neighbor list is used, only the water atoms close to the ligand will be requested at each step.
\warning
Notice that the calculation of the neighbour list is not not parallelized for \ref COORDINATION and \ref DHENERGY.
As a consequence, if you run
with many processors and/or OpenMP threads, the neighbor list might even make the calculation slower.
\page Openmp OpenMP
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