!-----------------------------------------------------------------
! This file is part of
!
!  Trajman: A MD Trajectory Analysis Tool
!
!  Copyright (C) 2010-2014, Jon Kapla, kaplajon@gmail.com
!
! Trajman is free software: you can redistribute it and/or modify
! it under the terms of the GNU General Public License as published by
! the Free Software Foundation, either version 3 of the License, or
! (at your option) any later version.
!
! Trajman is distributed in the hope that it will be useful,
! but WITHOUT ANY WARRANTY; without even the implied warranty of
! MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
! GNU General Public License for more details.
!
! You should have received a copy of the GNU General Public License
! along with Trajman.  If not, see <http://www.gnu.org/licenses/>.
!-----------------------------------------------------------------

TRAJMAN: A MD TRAJECTORY ANALYSIS TOOL

Trajman is a linux based molecular dynamics trajectory analysis
tool written in fortran. It is mainly aimed towards analysis of
simulations of model lipid membranes, but can easily be adopted
for other use as well.

Get Trajman source code:

Trajman source code can be downloaded with git:

> git clone git@github.com:kaplajon/trajman.git

Since the program is in constant development it might be wise
to check the commit log for suitable revisions and changes.

> git log

Dependencies:

Trajman needs the Visual Molecular Dynamics molfile_plugin to
be functional. There is a version of the molfile_plugin 
in the trajman build dir. You have also the possibility to 
download and build the latest version from:

http://www.ks.uiuc.edu/Research/vmd/

Make sure you also compile the fortran c wrapper located in 
the molfile_plugin/f77 folder.

For more information about of the vmd plugins, please see the vmd homepage.

In ubuntu the following command should pull all dependencies needed for
the trajman build including git and gfortran:

> sudo apt-get install tcl8.5-dev libnetcdf-dev build-essential gfortran git

BUILD EXAMPLE:

Compile vmd plugins (Please read the license file in the
vmd_plugins1.9 dir):

> cd vmd_plugins1.9
> make LINUXAMD64 TCLINC=-I/usr/include/tcl8.5 TCLLIB=-F/usr/lib
> cd molfile_plugin/f77
> make ARCH=LINUXAMD64 FC=gfortran TCLLIB=-L/usr/lib NETCDFLIB=-L/usr/lib TCLLDFLAGS=-ltcl8.5 f77_molfile.o

When you have VMD plugins compiled. Compile trajman by telling
make where your VMD plugins are situated, and what archflag you
used. Note that you need gfortran. Here's a 64-bit example:

make VMD_ARCH=LINUXAMD64 VMD_PLUGINS=vmd_plugins1.9/
(or set the environment variables in the Makefile directly and use 'make')

Run trajman -h for more information about usage.