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README.md

README.md

g_amide

OVERVIEW

The program g_amide is a post-processing tool for use with the GROMCAS (www.gromacs.org) molecular dynamics (MD) simulation package. The program allows the user to predict Amide I vibrational frequencies and coupling parameters for individual peptide amide groups as a function of time along an MD trajectory. In conjunction with the sister program g_spec (in preparation for release on github), the program allows the user to predict Amide I vibrational spectra for different protein structures, allowing the user to link MD simulation ensembles with experimental spectroscopic data.

g_amide uses a set of electrostatic- and dihedral-based maps for frequency and coupling constant calculations. For an overview of these methods see [Reppert and Tokmakoff, J Chem Phys. 142, 125104 (2015)]. In works that make use of the g_amide source code, we ask that you cite both the relevant spectroscopic map (see README.txt file in the maps subdirectory) and the following review article:

"Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics". Ann. Rev. Phys. Chem. Vol. 67 (2016), in press. DOI: 10.1146/annurev-physchem-040215-112055

The program calls GROMACS libraries for file parsing and so requires a local gromacs installation to be accessible (see www.gromacs.org). Compiling the code requires access to the gromacs home installation directory including the gromacs lib/ and include/gromacs directories. The lib/directory should contain a libgmx.so file which links to the installed gromacs libraries, while the include directory should contain a variety of *.h header files. In a default gromacs installation, the home directory is just /usr/local/gromacs and contains the lib/ and include/gromacs/ directories.

INSTALLATION

To install the program:

(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_amide 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_amide/

(1) Prepare the Makefile.

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

vi src/Makefile

Modifications should be required for only the first four lines. Default settings are pasted below.

CC=gcc
OMP_PARALLEL=FALSE
LIB_DIR=/usr/local/gromacs/lib
INC_DIRS=/usr/local/gromacs/include/gromacs/

The first line specifies a C compiler. The gcc compiler should be available on most linux systems; in this case no change is necessary.

The second line specifies whether or not parallelization should be enabled. g_amide has the ability to use OpenMP libraries to parallelize computation (i.e. parameters are calculated for multiple bonds simultaneously using multiple cores). To use this capability, a working installation of OpenMP must be available, and the flag OMP_PARALLEL must be set to TRUE. The default setting of FALSE does not require the presence of OpenMP libraries, but will not carry out calculations in parallel.

The final two lines specify the gromacs lib and include directories already discussed. In general, these lines should read

LIB_DIR=<gromacs home>/lib
INC_DIRS=<gromacs home>/include/gromacs/

where specifies the home directory of your local gromacs installation.

(2) Compile the code.

Once the Makefile has been modified, type at the command line (still in the g_amide directory)

make -C src/

to compile the code located in the g_amide/src directory. This should produce a binary file called g_amide, which can be called from the command line.

(3) Add the binary file to the user path.

To make this program accessible outside the installation directory, it should be added to the user path. This can be achieved either by copying the file to a directory already in the path (e.g. /home//bin) or by adding the g_amide/src directory to the user path. If modifying the path, you may wish to do so in a startup file which is executed every time a user logs onto the system. For example, for the example above, one might append the line

PATH=$PATH:/home/mike/apps/g_amide/src/

to the file ~/.bashrc, so that the program src directory will be added to the path every time the user logs onto the system.

(4) Run a test calculation!

To run a test calculation, follow the instructions in TUTORIAL.txt in the g_amide/test directory.