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Martin Kurečka
Plumed AlphaFold
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9ab5f71d
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9ab5f71d
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8 years ago
by
Giovanni Bussi
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added notes on metad
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user-doc/Performances.txt
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@@ -68,8 +68,25 @@ mpiexec -np 4 gmx_mpi mdrun -nb gpu -ntomp 1 -pin on -gpu_id 0011
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@@ -68,8 +68,25 @@ mpiexec -np 4 gmx_mpi mdrun -nb gpu -ntomp 1 -pin on -gpu_id 0011
\page Metadyn Metadynamics
\page Metadyn Metadynamics
TO DO
Metadynamics can be sped up significantly using grids,
which are activated setting the GRID_MIN and GRID_MAX keywords of \ref METAD.
This makes addition of a hill to the list a bit slower (since
the Gaussian has to be evaluated for many grid points)
but the evaluation of the potential very fast. Since
the latter is usually done every few hundred steps, whereas the former
typically ad every step, using grids will make the simulation
much faster.
Notice that when restarting a simulation the history is read by default
from a file and hills are added again to the grid.
This allows one to change the grid boundaries upon restart. However,
the first step after restart is usually very slow.
Since PLUMED 2.3 you can also store the grid on a file
and read it upon restart. This can be particularly
useful if you perform many restarts and if your hills file has
become very large.
For the precise syntax, see \ref METAD
\page MTS Multiple time stepping
\page MTS Multiple time stepping
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