QM/MM documentation in user guide
[namd.git] / ug / ug.tex
1 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
2 %                                                                          %
3 %              (C) Copyright 1995 The Board of Trustees of the             %
4 %                          University of Illinois                          %
5 %                           All Rights Reserved                            %
6 %                                                                          %
7 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
8
9 \documentclass[11pt]{article}
10 \usepackage{graphicx, caption}
11 \usepackage{makeidx}
12 \usepackage{amssymb}
13 \usepackage{amsmath}
14 \usepackage{verbatim}
15 \usepackage{comment}
16 \usepackage[stable]{footmisc}
17 \usepackage[pagebackref,colorlinks,citecolor=blue,hyperfootnotes=false]{hyperref}  % links in table of contents
18 %\usepackage{tocloft}
19 \makeindex
20
21 % define margins, etc
22 \topmargin      0.1in
23 \oddsidemargin  0in
24 \evensidemargin 0in
25 \textheight     8.80in
26 \textwidth      6.50in
27 \marginparsep   0.25cm
28 \headheight     0in
29 \headsep        0in
30 %\footskip      0.5in
31 %\footheight    0in%
32
33 % define macros
34 \input{namd_macros}
35 \input{ug_macros}
36 \input{psfgen_macros}
37
38 \includecomment{cvnamd}
39 \excludecomment{cvlammps}
40 \excludecomment{cvrefman}
41 \input{ug_colvars_macros}
42
43 \setcounter{secnumdepth}{3}
44 %% \setcounter{tocdepth}{5} %% very detailed table of contents
45 \setcounter{tocdepth}{4}
46
47 %
48 % the document itself
49 %
50
51
52 \begin{document}
53
54 % strictly enforce margins rather than complaining
55 \sloppy
56
57 % initial pages for the guide - title, TOC, etc.
58 \input{namd_begindoc}
59
60 % Introduction
61 \input{ug_intro}
62
63 % Getting started
64 \newpage
65 \input{ug_start}
66
67 % Input and output files
68 \newpage
69 \input{ug_io}
70
71 % Making PSF files
72 \newpage
73 \input{ug_psfgen}
74
75 % Force field parameters
76 \newpage
77 \input{ug_forcefield}
78
79 % Implicit Solvent Parameters
80 \newpage
81 \input{ug_gbis}
82
83 % Standard minimization and dynamics parameters
84 \newpage
85 \input{ug_dynamics}
86
87 % Performance tuning parameters
88 \newpage
89 \input{ug_performance}
90
91 % User defined forces
92 \newpage
93 \input{ug_userdef}
94
95 % Free energy of conformation change calculations
96 % \newpage
97 % \input{ug_fenergy}
98
99 % Collective variable-based calculations
100 \newpage
101 \input{ug_colvars}
102
103 % Extended adaptive biasing force method - now covered in colvars docs
104 % \input{ug_eabf}
105
106 % Alchemical free energy perturbation calculations
107 \newpage
108 \input{ug_alchemy}
109
110 % Accelerated sampling methods
111 \newpage
112 \input{ug_accel}
113
114 % Go simulation methods
115 \newpage
116 \input{ug_go}
117
118 % constant pH
119 \newpage
120 \input{ug_constantph}
121
122 % QM/MM
123 \newpage
124 \input{ug_qmmm}
125
126 % Runtime analysis
127 \newpage
128 \input{ug_analysis}
129
130 % Equivalence with X-PLOR parameters
131 \newpage
132 \input{ug_xplor}
133
134 % Sample configuration files
135 \newpage
136 \input{ug_sample}
137
138 % Description of how to run namd
139 \newpage
140 \input{ug_runit}
141
142 % How to get and install namd
143 \newpage
144 \input{ug_avail}
145
146 % NOTE: with hyperref package, \contentsline needs 5 arguments, not 3.
147 % https://tex.stackexchange.com/questions/168013/redefining-contentsline-with-hyperref-loaded
148 \newpage
149 \addtocontents{toc}{\protect\contentsline{section}{References}{\thepage}{}{}} 
150 \bibliographystyle{abbrv}
151 \bibliography{ug,ug_colvars,ug_eabf}
152
153 \newpage
154 \addtocontents{toc}{\protect\contentsline{section}{Index}{\thepage}{}{}}
155 \printindex
156
157 % that's all, folks
158 \end{document}
159