--- /dev/null
+\documentclass[12pt]{article}
+%\usepackage{latex2html}
+\usepackage{enumerate}
+\usepackage{longtable}
+\usepackage{hyperref}
+\usepackage{amsmath}
+\usepackage{color}
+\parindent=0pt
+\parskip=12pt
+\textheight=24cm
+\textwidth=18cm
+\topmargin=-2.5cm
+\oddsidemargin=-0.5cm
+\setcounter{secnumdepth}{5}
+\setcounter{tocdepth}{5}
+\begin{document}
+\sloppy
+
+\title{UNRES.3.2.1 -- INSTALLATION GUIDE}
+
+\author{Dawid Jagie{\l}a, Adam Liwo\\ Laboratory of Molecular Modeling\\ Faculty of Chemistry\\ University of Gdansk\\ Wita Stwosza 63\\ 80-308 Gdansk, Poland}
+
+\maketitle
+
+\newpage
+
+\tableofcontents
+
+\newpage
+
+\section{Putting the package on your system}
+\label{section:put}
+
+The distribution is contained in the unrespack-v.3.2.1.tar.gz file. To put the package
+on your system, copy the archive to your UNRES directory (you might want to create
+an environmental variable, \$UNRESROOT or so, to define the location of UNRES on
+your system) and say:
+
+\begin{verbatim}
+gzip -cd unrespack-v.3.2.1.tar.gz | tar xf -
+\end{verbatim}
+
+This will produce the directory structure shown in Figure \ref{fig:distr}.
+
+\begin{figure}
+{\small
+\begin{verbatim}
+$UNRESROOT
+ |
+ |---------doc (documentation)
+ |
+ |---------PARAM (force field parameters)
+ |
+ |---------source
+ | |
+ | |-----unres (UNRES source codes; various versions)
+ | | |
+ | | |---src_MIN (only energy evaluation and minimization)
+ | | |---src_CSA (all functions except MD, includes CSA)
+ | | |---src_MD (all functions except CSA, includes MD, single chains)
+ | | |---src_MD-M (all functions except CSA, includes MD, oligomeric proteins)
+ | |-----wham (weighted analysis method source codes)
+ | | |
+ | | |---src (single chains)
+ | | |---src-M (oligomeric proteins)
+ | |
+ | |-----cluster (cluster analysis source coded)
+ | | |
+ | | |---clust-unres
+ | | | |
+ | | | |----src (input data from UNRES)
+ | | |
+ | | |---clust-wham (input data from WHAM)
+ | | |
+ | | |----src (for single-chain proteins)
+ | | |----src-M (for oligomeric proteins)
+ | |
+ | |-----xdrfpdb (file format conversion source codes)
+ | |
+ | |---src (single chains)
+ | |---src-M (oligomers)
+ |
+ |----------bin (C-shell script, batch scripts, and pre-compiled binaries)
+ | |
+ | |-----unres
+ | | |
+ | | |---CSA
+ | | |---MD
+ | |
+ | |-----wham
+ | |-----cluster
+ | |-----xdrfpdb
+ |
+ |--------examples
+ |
+ |-----unres
+ |-----wham
+ |-----cluster
+\end{verbatim}
+}
+\caption{Directory structure of the unres-3.2.1 package}
+\label{fig:distr}
+\end{figure}
+
+\section{Installation options}
+\label{sect:general}
+
+The most convenient way to install the package is using Cmake, as described
+in section 2. If your system does not run the required version of Cmake or
+installation does not work, do step-by-step compilation of the components
+of the package, as described in section 3.
+
+\subsection{Requirements}
+
+\begin{description}
+\item{--} C compiler
+\item{--} Fortran compiler (must understant the Fortran 77 instructions)
+\item{--} MPI (for CSA and MREMD)
+\end{description}
+
+\section{Installation using Cmake}
+\label{section:Cmake}
+
+\subsection{Requirements}
+
+\begin{description}
+\item{--} CMake 2.8.0 or later
+\item{--} C compiler
+\item{--} Fortran compiler
+\item{--} MPI (for CSA and MREMD)
+\end{description}
+
+\subsection{Basic installation}
+
+These instructions give a very basic overview of how to configure, compile and
+install UNRESPACK on most systems. If you are using unique install locations
+and/or libraries that are not automatically detected please consult the 'Advanced'
+section.
+
+\begin{enumerate}
+
+\item
+Create a 'build' directory in the package source directory.
+
+\begin{verbatim}
+ mkdir build
+ cd build
+\end{verbatim}
+
+\item
+Configure the build system
+
+\begin{verbatim}
+ cmake ..
+\end{verbatim}
+
+\item
+Compile
+
+\begin{verbatim}
+ make
+\end{verbatim}
+
+\item
+Install
+
+\begin{verbatim}
+ sudo make install
+\end{verbatim}
+
+\noindent or
+
+\begin{verbatim}
+ make install
+\end{verbatim}
+
+\end{enumerate}
+
+\subsection{Advanced installation}
+
+The build system (CMake) provides mechanisms for specifying non-standard
+build parameters.
+
+\begin{enumerate}
+
+\item
+\underline{Compilers \& installation}
+
+\begin{verbatim}
+ -DCMAKE_Fortran_COMPILER=xxx equal to name of Fortran Compiler you wish to use
+ (ifort, gfortran)
+
+ -DCMAKE_INSTALL_PREFIX=xxx specify the binaries installation prefix
+ (default UNRESPACK_source_dir/bin)
+\end{verbatim}
+
+\item
+\underline{Force fields}
+
+\begin{verbatim}
+ -DUNRES_MD_FF=xxx compiles the MD versions with given force field.
+ Options are: GAB, E0LL2Y. Default: GAB
+
+ -DUNRES_CSA_FF=xxx compiles the CSA versions with given force field
+ Options are: CASP3, ALPHA, BETA, ALPHABETA, CASP5, 3P, 4P. Default: 4P.
+\end{verbatim}
+
+Please read the online documentation on force fields available at
+ http://unres.eu/unres\#SECTION00090000000000000000
+
+
+\item
+\underline{MPI}
+
+MPI implementation on your system should be automatically detected ("MPI Found"
+message after runing cmake). If not you have two options:
+
+\begin{enumerate}
+
+\item
+Try setting the path to you MPI wrapper implementation
+
+\begin{verbatim}
+ -DMPI_Fortran_COMPILER=xxx MPI wrapper
+\end{verbatim}
+
+\item
+If option 1 fails or your MPI implementation does not come with a compiler wrapper
+ try setting both the MPI include and library paths manually. This will circumvent
+ autodetection entirely.
+
+\begin{verbatim}
+ -DMPI_Fortran_INCLUDE_PATH=xxx
+ -DMPI_Fortran_LIBRARY="xxx"
+\end{verbatim}
+
+\end{enumerate}
+\end{enumerate}
+
+\section{Step-by-step installation}
+\label{sect:stepbystep}
+
+For this installation, you will need to visit each source directory (see doc/UNRESPACK.txt
+for directory structure). Specific installation instructions are in the documentation of
+of the particular components of the package (UNRES, WHAM, CLUSTER, XDRFPDB). Only general
+instructions are given here.
+
+\begin{enumerate}
+
+\item
+Go to the respective source directory.
+
+\item
+Determine if any of the Makefiles present there matches your needs. The Makefiles for
+Intel Fortran and Gnu Fortran are present everywhere and are guaranteed to work (provided
+that your compiler/MPI installation is correct). Use this Makefile as the working Makefile
+
+If your system uses a different compiler, copy the most matching Makefile to your working
+Makefile (e.g., to Makefile\_CRAY if you'll be working with Cray Fortran).
+
+\item
+Make a symbolic link of the working Makefile to Makefile, e.g.,
+
+\begin{verbatim}
+ln -s Makefile_gfortran Makefile
+\end{verbatim}
+
+Before that, you'll need to remove the existing symbolic link (in the distribution, it
+points to Makefile\_ifort).
+
+\item
+Edit the Makefile to define MPI location, libraries, and the binaries directory
+and executalble names, if you want to use different location/names from those in the
+distribution Makefiles. The present locations are the subdirectories of the bin
+directory and executable names include package component, compiler, MPI information,
+and force field, e.g. unres\_csa\_gfort\_MPICH\_4P.exe stands for the CSA component,
+compiled with GNU Fortran in a parallel mode (using MPICH) to run calculations with
+the 4P force field.
+
+\item
+For the components of XDRFPDB and in the directory cluster/unres/src, say
+
+\begin{verbatim}
+make
+\end{verbatim}
+
+In other directories say
+
+\begin{verbatim}
+make <force_field>
+\end{verbatim}
+
+to create the respective executable.
+
+The compiler flags are specified for the 4P (also covers the 3P, and CASP5 ff),
+GAB (also covers E0G), and E0LL2Y force fields for all components; the CASP3 force field
+is also specified for the CSA and MINIM component.
+\end{enumerate}
+
+\section{TECHNICAL SUPPORT CONTACT INFORMATION}
+\label{sect:support}
+
+ Dawid Jagie{\l}a\\
+ Faculty of Chemistry, University of Gdansk\\
+ ul. Wita Stwosza 63, 80-308 Gdansk Poland.\\
+ fax: +48 58 523 5012\\
+ e-mail: \href{mailto:lightnir@gmail.com}{lightnir@gmail.com}\\
+
+\small{
+ Prepared by Dawid Jagie{\l}a and Adam Liwo, 4/12/2014\\
+}
+
+\end{document}
projects / unres.git / blobdiff