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README.md

README.md

g_spec

g_spec is a spectral simulation program for converting molecular energy and dipole trajectories into simulated linear and nonlinear optical spectra. In conjunction with the open-source program g_amide, it enables the user to translate structural trajectories from a molecular dynamics (MD) simulation in the GROMACS simulation package (www.gromacs.org) into Amide I (backbone carbonyl stretch) vibrational spectra.

The basic input to the g_spec program is a set of text files providing a trajectory of exciton-like Hamiltonians and transition-dipole moment vectors. In the context of protein Amide I calculations, such files can be generated using the g_amide program referenced above. Using this input, g_spec simulates linear absorption and nonlinear (two-dimensional) spectroscopic signals using a variety of methods.

DEPENDENCIES

g_spec calls several external libraries in its function. These libraries MUST be available during installation or the code will not compile:

(1) A working GROMACS installation for MD simulations. (See www.gromacs.org).

(2) A functional installation of FFTW3 for fast Fourier transforms (see www.fftw.org).

(3) Working LAPACK and LAPACKE libraries for linear algebra processing (see www.netlib.org/lapack).

(4) Working BLAS libraries for linear algebra processing (see www.netlib.org/blas).

Although not required, g_spec can also make use of OpenMP libraries to implement a certain level of parallelization into the calculation. To make use of these features, a working OpenMP installation must also be available.

INSTALLATION

(0) Choose an installation directory.

This may be any directory where you have read/write permissions, but should be a permanent installation location (e.g. not your user download folder). For example, if your username is mike, you might wish to install the program in an "apps" directory such as /home/mike/apps/. Move the g_spec directory (where this README.txt file is located) into the chosen installation directory and at the command prompt cd to that location, e.g. in our example

    cd /home/mike/apps/g_spec/

(1) Prepare the Makefile.

The Makefile specifies machine parameters for compiling the code. Two alternative makefiles are included in this distribution. The default file named simple "Makefile" makes use of the gcc C-language compiler, installed onmost linux-based operating systems. The second, Makefile_icc is configured for compilation with the intel icc compiler. This compiler is able to optimized the g_spec installation in a fashion that make make it run faster on some systems. If the icc compiler is available on your system, we recommend using it. To do so, enter at the command line

cp Makefile_icc Makefile

Note that a backup copy of the gcc makefile is stored as Makefile_gcc if you wish to rever to gcc installation.

Next, modify the Makefile. E.g. to open the file using vi, type at the console

    vi src/Makefile

Modifications should be required onlyin the first four lines of the file. Three lines should be checked.

First, the flag OMP_PARALLEL should be set to either "TRUE" or (by default) "FALSE". If set to true, this flag enables parallel processing using the OpenMP library. Parallel processing will enable to code to execute calculations faster if multiple processors are available, but installation requires an OpenMP package accessible during compilation. (This is the -lgomp flag under the LIBFLAGS variable in the Makefile). If you do not have an OpenMP library available (or do not know how to access it), leave the flag set to FALSE.

Second, the GROMACS_DIR flag should be set to the absolute path of your GROMACS installation directory, e.g. /home/mike/apps/gromacs/.

Finally, the LAPACK_DIR flag must be set to the absolute path of the LAPACK installation directory, e.g. /home/mike/apps/lapack. Note that this package must include the lapacke header files for linking with C code.

(2) Compile the code. In the same directory as your Makefile and source code enter at the command line

make 

The make program should locate and read your Makefile and the selected compiler will compile the code. If you encounter errors, check that the various libraries (-lxxx flags) and included header files (-I flags) are available to the system. If you encounter difficulties, try using the simplest settings possible first, using the gcc compiler (assuming it is available on your system) with OMP_PARALLEL set to FALSE.

(3) Run a test calculation! A set of example input files is included in the directory g_spec/test/input, along with a brief tutorial describing basic syntax for the program.