From 6f2cde4b066ee24ce3a821b1358a8fd569694944 Mon Sep 17 00:00:00 2001 From: Alexey Shvetsov Date: Wed, 23 Nov 2011 15:30:38 +0400 Subject: [PATCH] Make manual consistent with renamed mdp opetion names Signed-off-by: Alexey Shvetsov --- forcefield.tex | 12 ++++++------ special.tex | 6 +++--- 2 files changed, 9 insertions(+), 9 deletions(-) diff --git a/forcefield.tex b/forcefield.tex index 6449c7d..b4302aa 100644 --- a/forcefield.tex +++ b/forcefield.tex @@ -2346,13 +2346,13 @@ rvdw = 0.9 rlist = 0.9 rcoulomb = 0.9 fourierspacing = 0.6 -ewald_rtol = 1e-5 +ewald-rtol = 1e-5 \end{verbatim} The {\tt fourierspacing} parameter times the box dimensions determines the highest magnitude of wave vectors $m_x,m_y,m_z$ to use in each direction. With a 3-nm cubic box this example would use $11$ wave vectors -(from $-5$ to $5$) in each direction. The {\tt ewald_rtol} parameter +(from $-5$ to $5$) in each direction. The {\tt ewald-rtol} parameter is the relative strength of the electrostatic interaction at the cut-off. Decreasing this gives you a more accurate direct sum, but a less accurate reciprocal sum. @@ -2387,12 +2387,12 @@ rvdw = 0.9 rlist = 0.9 rcoulomb = 0.9 fourierspacing = 0.12 -pme_order = 4 -ewald_rtol = 1e-5 +pme-order = 4 +ewald-rtol = 1e-5 \end{verbatim} In this case the {\tt fourierspacing} parameter determines the maximum -spacing for the FFT grid and {\tt pme_order} controls the +spacing for the FFT grid and {\tt pme-order} controls the interpolation order. Using fourth-order (cubic) interpolation and this spacing should give electrostatic energies accurate to about $5\cdot10^{-3}$. Since the Lennard-Jones energies are not this @@ -2487,7 +2487,7 @@ done by default since it takes a couple of minutes, but for large runs it will save time. Turn it on by specifying \begin{verbatim} -optimize_fft = yes +optimize-fft = yes \end{verbatim} in your {\tt .mdp} file. diff --git a/special.tex b/special.tex index b8c3fcf..6044ffa 100644 --- a/special.tex +++ b/special.tex @@ -666,7 +666,7 @@ rvdw = 1.0 \end{verbatim}} {\tt mdrun} will read a single non-bonded table file, -or multiple when {\tt energygrp_table} is set (see below). +or multiple when {\tt energygrp-table} is set (see below). The name of the file(s) can be set with the {\tt mdrun} option {\tt -table}. The table file should contain seven columns of table look-up data in the order: $x$, $f(x)$, $-f'(x)$, $g(x)$, $-g'(x)$, $h(x)$, $-h'(x)$. @@ -692,11 +692,11 @@ Lennard-Jones potentials combined with a normal Coulomb. If you want to have different functional forms between different groups of atoms, this can be set through energy groups. Different tables can be used for non-bonded interactions between -different energy groups pairs through the {\tt .mdp} option {\tt energygrp_table} +different energy groups pairs through the {\tt .mdp} option {\tt energygrp-table} (see \secref{mdpopt}). Atoms that should interact with a different potential should be put into different energy groups. -Between group pairs which are not listed in {\tt energygrp_table}, +Between group pairs which are not listed in {\tt energygrp-table}, the normal user tables will be used. This makes it easy to use a different functional form between a few types of atoms. -- 1.7.8.rc3