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small docs updated
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carlocamilloni committed Jul 5, 2023
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Expand Up @@ -82,7 +82,7 @@ mpiexec -np 2 gmx_mpi mdrun -nb gpu -ntomp 2 -pin on -gpu_id 01
\page Metadyn Metadynamics

Metadynamics can be sped up significantly using grids,
which are activated setting the GRID_MIN and GRID_MAX keywords of \ref METAD.
which are activated setting the GRID_MIN and GRID_MAX keywords of \ref METAD and \ref PBMETAD.
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
Expand All @@ -98,7 +98,7 @@ 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 are large.

For the precise syntax, see \ref METAD
For the precise syntax, see \ref METAD and \ref PBMETAD

\page MTS Multiple time stepping

Expand Down Expand Up @@ -220,7 +220,7 @@ This is particularly true for the calculation of beta structures.

The FIRST thing to speed up \ref PARABETARMSD and \ref ANTIBETARMSD is to use the keyword
STRANDS_CUTOFF (i.e. STRANDS_CUTOFF=1), in this way only a subset of possible fragments, the one
less than 1. nm apart, are used in the calculation.
less than 1.0 nm apart, are used in the calculation.

The metric used to calculate the distance from ideal secondary structure elements can also influence
the performances, try to use TYPE=OPTIMAL or TYPE=OPTIMAL-FAST instead of TYPE=DRMSD.
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Found broken examples in automatic/performance-optimization.txt
Found broken examples in automatic/a-trieste-6.txt
Found broken examples in automatic/munster.txt
Found broken examples in automatic/ANN.tmp
Found broken examples in automatic/EDS.tmp
Found broken examples in automatic/EMMI.tmp
Found broken examples in automatic/ENVIRONMENTSIMILARITY.tmp
Found broken examples in automatic/FOURIER_TRANSFORM.tmp
Found broken examples in automatic/FUNCPATHGENERAL.tmp
Found broken examples in automatic/FUNCPATHMSD.tmp
Found broken examples in automatic/FUNNEL.tmp
Found broken examples in automatic/FUNNEL_PS.tmp
Found broken examples in automatic/GHBFIX.tmp
Found broken examples in automatic/INCLUDE.tmp
Found broken examples in automatic/MAZE_MEMETIC_SAMPLING.tmp
Found broken examples in automatic/MAZE_OPTIMIZER_BIAS.tmp
Found broken examples in automatic/MAZE_RANDOM_ACCELERATION_MD.tmp
Found broken examples in automatic/MAZE_RANDOM_WALK.tmp
Found broken examples in automatic/MAZE_SIMULATED_ANNEALING.tmp
Found broken examples in automatic/MAZE_STEERED_MD.tmp
Found broken examples in automatic/PIV.tmp
Found broken examples in automatic/PLUMED.tmp
Found broken examples in MiscelaneousPP.md

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