This is AMBER8.  All contents are protected by Copyright and Licensing 
provisions.  See the Web page below for licensing information; using or
running this code without a valid license is prohibited.

A "roadmap" for installing and testing things is in the file INSTALL.  All
of the documentation is in the "doc" directory, in the *.pdf files.
The file KNOWN_PROBLEMS should be consulted.

For more information, including tutorials, bug reports, etc., please consult
the Amber Web page:

               http://amber.scripps.edu

INSTALL on IBM Systems:

Complete documentation, including installation instructions are in the
amber8.pdf file in the "amber8/doc" directory, created in step "0", below.
Here is a brief roadmap for the installation process:

0.  Unpack the files from the CD-ROM:

    Go to a working directory in which you have at least 300 Mb of free
    space; in our example, this will be "/usr/local", but it could be  
    anywhere. Unpack the distribution:

       cd /usr/local
       gunzip -c /mnt/cdrom/amber8.tgz | tar xvf -

	(This assumes that your CD-ROM is mounted at /mnt/cdrom).  This will
	create a /usr/local/amber8 directory.  If you wish, you can also upack
    MOIL-View at this time (cf. step 6 below):

       gunzip -c /mnt/cdrom/mview11.tgz | tar xvf -

    The tutorials are quite large (about 250 Mbytes when uncompressed), 
    so we have placed them in a separate tar file, even though disk space 
    is cheap these days.  If you have room:

       gunzip -c /mnt/cdrom/tutorial.tgz | tar xvf -

1.  Set up your environment:

    The AMBERHOME environment variable should point to the directory
    you are now in.  For example:

    Using csh, tcsh, etc:   setenv AMBERHOME  /usr/local/amber8

    Using sh, bash, zsh, etc: set AMBERHOME=/usr/local/amber8
                              export AMBERHOME

    NOTE:  Be sure to replace the "/usr/local" part above with whatever
    path is appropriate for your machine.

    You must add $AMBERHOME/exe to your PATH environment variable.

2.  Compile the basic AMBER distribution for a single cpu:

    a. go to the src directory below this one.
           cd $AMBERHOME/src

    b. run the configuration script:

           ./configure xlf90_aix         for AIX on POWER with xlf compiler
           ./configure xlf90_suse        for SUSE on POWER with xlf compiler

           (./configure --help will give instructions and options;
           At this point, do not specify any of the parallel options.)

           You may wish to examine (and edit) the config.h file at this point.

    c. compile and install the binaries into $AMBERHOME/exe:

           make serial

3.  Test the basic AMBER distribution

           cd $AMBERHOME/test
           make test

    See the Users' Manual for comments on interpreting the test suite.

4.  (Optional) Compile the code for parallel execution:

    If you want to run sander, sander.LES, or pmemd in a parallel
    environment, do the following:

            cd $AMBERHOME/src
            make clean
            ./configure -mpi xlf90_aix        ( AIX  POWER)
            ./configure -mpich xlf90_suse     ( SUSE POWER )
            make parallel

            ***** AIX MPI *****

            run_ibm_mpi provides a simple script for running parallel
            sander using IBM MPI.  It assumes that the running directory
            was created in $AMBERHOME/test.

            In this example,

            MP_PROCS        ! requests a 16-way run
            MP_HOSTFILE     ! a file with a list nodes where the job 
                            ! is going to run
            MP_SHARED_MEMORY! required for better performance on shared-memory
                            ! IBMs
            MP_WAIT_MODE    ! required for better performance on shared-memory
                            ! IBMs

*  For information on the sander options, see AMBER manual
       
           ***** SUSE MPICH *****

            You can then test the MPICH parallel version.  
            Set the DO_PARALLEL environment varialbe to 
            something like 'mpirun -np 4 ' Then

            cd $AMBERHOME/test
            make test.parallel

    If you are planning to run periodic, explicit solvent simulations using
    the paricle-mesh Ewald (PME) method, you will want to compile the
    pmemd program.  See $AMBERHOME/src/pmemd/README for instructions.

5.  Documentation

    The Users' manual is in $AMBERHOME/doc/amber8.pdf.  Point your browser 
    to $AMBERHOME/tutorials/index.html to access tutorial information.

    A variety of input and output files can also be found in the test
    and examples subdirectories.

6.  MOIL-view

    The CD-ROM also contains a distribution of the MOIL-view program, which
    can be used to visualize Amber structures and trajectories.  Un-tar this
    file and follow the instructions to install.  Note: MOIL-view requires GL
    (not openGL), and so effectively requires an SGI machine.