File	Date	Author	Commit
doc	2012-01-17	Diamantis Sellis	[fde61e] added screenshot files
icons	2011-03-12	Diamantis	[93dfcd] version 1_09
water	2011-03-12	Diamantis	[93dfcd] version 1_09
.gromita.defaults	2012-05-07	Diamantis Sellis	[6e369a] fix bug with vector type data (e.g. coordinetes...
README	2012-05-07	Diamantis Sellis	[68ef66] recover changes from chrashed system
gromita.pl	2012-05-07	Diamantis Sellis	[68ef66] recover changes from chrashed system
options.csv	2011-07-04	Diamantis Sellis	[de8793] invoke term in more options in genion
options.ods	2011-07-04	Diamantis Sellis	[de8793] invoke term in more options in genion
publish.sh	2011-07-07	Diamantis Sellis	[3d15ef] tar file is named %y%m%d for easier sorting
setup.pl	2012-05-07	Diamantis Sellis	[68ef66] recover changes from chrashed system
variable.pm	2012-05-07	Diamantis Sellis	[6e369a] fix bug with vector type data (e.g. coordinetes...

Read Me

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( (_-. )   / )(_)(  )    (  _)(_   )(  /(__)\ 
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Gromita is a GUI for GROMACS. Details about Installation, Troubleshooting 
and usage can be found in the /doc directory.

GROMITA INSTALLATION INSTRUCTIONS

INSTALL PREREQUISITES
----------------------
1. Install the latest vesrsion of GROMACS (Gromita v.3.00 has been tested with GROMACS v.4.5.4) and the programs it depends on
2. Install Perl (in most Linux distributions it should be already installed)
3. Install Perl/Tk
   make sure that the CPAN module is installed
    $>perl -e 'use CPAN;'
   if it is installed no error message should appear.
   Switch user to root in order to make available perl/tk for all users and 
   invoke a CPAN shell
    $>su
    Password:
    #>perl -MCPAN -e shell
   (if you are using Ubuntu type instead: $>sudo perl -MCPAN -e shell and type
   your user password, not the root)
   install Perl/Tk:
    $>cpan>install Perl/Tk
   some installation and testing messages will follow, and when complete type
   quit to exit the CPAN shell

EXTRACT COMPRESSED FILE
-----------------------
3. Extract the compresed file (e.g in your desktop)
4. Open a terminal and cd to newly created directory

RUN SETUP
---------
5. In order to have gromita available for all users you must install gromita as root.

   $>su -c 'perl setup.pl'
   
   (if you are using Ubuntu try: $>sudo perl setup.pl)

      The setup script will check for the installed perl version, its
      modules, gromacs path e.t.c. Follow the instructions. Note that
      Gromita may complain about some version numbers, because it asks for
      the versions under wich it was developed. It will probably work well
      with much lower versions, but it has not been tested with them.

6. When the installation script is finished checking for installed programs
   it will ask for verification before proceeding. Note that the
   following steps must be done as root for gromita to be
   available to all users:
      Proceed with installation? [y/n] y
7. Gromita is ready! Just type gromita and it will load

GETTING STARTED
---------------
1. Create a working directory in which your files will be stored
2. Change directory to the file specified
3. Type gromita
4. Go to Options->Preferences and type your favorite molecular
   viewer (e.g. rasmol, pymol) and terminal (e.g. xterm, konsole)
   for gromita to use
5. Go to File->Open and load a pdb molecule
6. Use the main buttons to perform your first simulation


CITE
----
Sellis, D., D. Vlachakis, and M. Vlassi (2009). Gromita: A fully integrated graphical user interface to gromacs 4. Bioinformatics and Biology Insights  2009 (3), 99-102.

WEBSITE
-------
http://bio.demokritos.gr/gromita/