diff --git a/user-doc/Analysis.txt b/user-doc/Analysis.txt index bd8cb825d63c5b27664224f99f6e6bd00c89778a..5e03d3a2e668778246769bef263bc48c19765741 100644 --- a/user-doc/Analysis.txt +++ b/user-doc/Analysis.txt @@ -2,8 +2,9 @@ \page Analysis Analysis -Once you have calculated a number of collective variables PLUMED allows you to either analyse -your trajectory. The list of available on-the-fly analysis tools contains: +PLUMED can be used to analyse trajectories either on the fly during an MD run or via +postprocessing a trajectory using \ref driver. The following is a list of the various +methods for analysing trajectories contained in PLUMED. @ANALYSIS@ diff --git a/user-doc/Bias.txt b/user-doc/Bias.txt index 94b74914b16c7146af6eed4f09282b744535657e..7f6ae6a85dd42a7e1c50f562cafcdfb27698764e 100644 --- a/user-doc/Bias.txt +++ b/user-doc/Bias.txt @@ -2,13 +2,12 @@ \page Bias Bias -Once you have calculated a number of collective variables PLUMED allows you to -run a number of enhanced sampling algorithms. -The list of available enhanced sampling algorithms contains: +PLUMED allows you to run a number of enhanced sampling algorithms. +The list of enhanced sampling algorithms contained in PLUMED is as follows: @BIAS@ -Methods, such as \ref METAD, that introduce a history dependent bias can be restarted +Methods, such as \ref METAD, that work by introducing a history dependent bias can be restarted using the \subpage RESTART keyword You can also use PLUMED in conjunction with VMD's interactive MD module by taking diff --git a/user-doc/Intro.txt b/user-doc/Intro.txt index 165034fb6463cbcb44e7cd205591eb8565d6bdf0..cf3e94e2155e0a41f73919fdee7336e869c9766f 100644 --- a/user-doc/Intro.txt +++ b/user-doc/Intro.txt @@ -3,14 +3,15 @@ PLUMED is a plugin that works with a large number of molecular dynamics codes. It can be used to analyse features of the dynamics on-the-fly or to perform a wide variety of free energy methods. -The original PLUMED 1 was highly successful and had over 1000 users. PLUMED 2 \cite plumed2 constitues an +The original PLUMED 1 \cite plumed1 +was highly successful and had over 1000 users. PLUMED 2 \cite plumed2 constitues an extensive rewrite of the original in a way that makes it more modular and thus easier to implement new methods, more straightforward to add it to MD codes and hopefully simpler to use. This is the user manual - if you want to modify PLUMED or to understand how it works internally, have a look at the <a href="../../developer-doc/html/index.html"> developer manual </a>. -To know the difference between PLUMED 1 and PLUMED 2, and to -follow the development of PLUMED 2, you can checkout the detailed changelog: +To understand the difference between PLUMED 1 and PLUMED 2, and to +follow the development of PLUMED 2, you can look at the detailed changelog: - Changes for \ref CHANGES-2-0 A short tutorial explaining how to move from PLUMED 1 to PLUMED 2 is also available (see \ref moving)