From 0493ec1266ea10c365229c09313002f0042191c9 Mon Sep 17 00:00:00 2001 From: Carlo Camilloni Date: Wed, 5 Jul 2023 12:11:57 +0200 Subject: [PATCH] small docs updated --- user-doc/Performances.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/user-doc/Performances.md b/user-doc/Performances.md index f39a5872d5..a0ac763b37 100644 --- a/user-doc/Performances.md +++ b/user-doc/Performances.md @@ -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 @@ -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 @@ -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.