Implement user guide

[alexxy/gromacs.git] / docs / manual / algorithms.tex

diff --git a/docs/manual/algorithms.tex b/docs/manual/algorithms.tex
index 53f7cdb4a26fe63f6f7018b3c8ee55f3092cad4f..ac864521a44db0872ee320dc217dafe5a77cf05b 100644 (file)
--- a/docs/manual/algorithms.tex
+++ b/docs/manual/algorithms.tex
@@ -1,7 +1,7 @@
 %
 % This file is part of the GROMACS molecular simulation package.
 %
-% Copyright (c) 2013,2014, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
 % Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 % and including many others, as listed in the AUTHORS file in the
 % top-level source directory and at http://www.gromacs.org.
@@ -311,7 +311,7 @@ All non-bonded interactions between pairs of energy-monitor groups can
 be excluded\index{exclusions}
 \ifthenelse{\equal{\gmxlite}{1}}
 {.}
-{(see \secref{mdpopt}).}
+{(see details in the User Guide).}
 Pairs of particles from excluded pairs of energy-monitor groups
 are not put into the pair list.
 This can result in a significant speedup
@@ -1934,7 +1934,7 @@ lower frequencies.
 {\gromacs} can also write reduced-precision coordinates for a subset of
 the simulation system to a special compressed trajectory file
 format. All the other tools can read and write this format. See
-\secref{mdpopt} for details on how to set up your {\tt .mdp} file
+the User Guide for details on how to set up your {\tt .mdp} file
 to have {\tt mdrun} use this feature.
 
 % \ifthenelse{\equal{\gmxlite}{1}}{}{
@@ -3176,7 +3176,7 @@ but differing slightly between the three Born radii models.
 % LocalWords:  GROningen MAchine BIOSON Groningen GROMACS Berendsen der Spoel
 % LocalWords:  Drunen Comp Phys Comm ROck NS FFT pbc EM ifthenelse gmxlite ff
 % LocalWords:  octahedra triclinic Ewald PME PPPM trjconv xy solvated
-% LocalWords:  boxtypes boxshapes editconf Lennard mdpopt COM XTC TNG kT defunits
+% LocalWords:  boxtypes boxshapes editconf Lennard COM XTC TNG kT defunits
 % LocalWords:  Boltzmann's Mueller nb int mdrun chargegroup simplerc prefactor
 % LocalWords:  pme waterloops CH NH CO df com virial integrator Verlet vverlet
 % LocalWords:  integrators ref timepoint timestep timesteps mdp md vv avek NVE