#GridMAT-MD-Auto

Written by: Abhishek Acharya Research Associate Structural and Computational Biology Lab CSIR-Central Food Technological Research Institute Mysuru

For any queries and reporting problems with the script, send a mail to: abhi117acharya@gmail.com

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This program is an automated version of GridMAT-MD-parallel, a modified version of GridMAT-MD. This was originally developed by Bevan Lab, Virginia Tech.

Please read and cite the following reference:

W. J. Allen, J. A. Lemkul, and D. R. Bevan. (2009). GridMAT-MD:A Grid-based Membrane Analysis Tool for Use With Molecular Dynamics. J. Comput. Chem., 30 (12), 1952-1958

For bug fixes and release notes on GridMAT-MD, please see the following site: http://www.bevanlab.biochem.vt.edu/GridMAT-MD/bugs.html

The parallelized version has been written by: Venkatramanan Krishnamani (Univesity of Iowa).

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#About GridMAT-MD-Auto

This is a program written in python2 and works as a wrapper for the original program written in perl.

This program allows the analysis of GROMACS membrane simulation trajectories, similar to the original version. Additionally, it also writes the time evolution of APL and and bilayer thickness over the course of the simulation in standard xmgrace format.

The program takes 4 files as input. Two of them are provided with the package; these are input files that specify parameters for running the GridMAT-MD APL and thickness calculations. First is an input file for APL calculations while the second is for calculation of bilayer thickness. Using two seperate input parameter files allows the user to specify parameters separately for APL and Bilayer thickness calculation; the script automatically calculates both the parameters and saves appropriate output files.

Since the analysis requires extracting all the frames as gro file and produces outputs for each frame analysed, the outputs take much disk space. Therefore, the default beha- -vior of the program is to delete the frame-by-frame output files. The user can choose to keep these files by providing the --keep flag.

Additionally, user can choose the start and ending time for running the analysis on a subsection of the full trajectory file; a -skip flag is also provided to skip frames during analysis.

Another python script output_avg.py is also provided to the users. This script taken the output .xvg files produced by GridMAT-MD-Auto and calculates the ensemble average value of the property with variance. Optionally, the Isothermal Area Compressibility Modulus value, derived from the calculated variance in APL is also printed to the output.

THe perl script, GridMAT-MD-parallel.pl provided with this distribution can also be used to run the calculations on a coordinte file in gro format.For usage see below. However for obtaining the xmgrace plots of APL and Bilayer thickness, you need to run the python script.

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#Usage

GridMAT-MD-Auto.py [-h] [-b BTIME] [-e ETIME] [-s SUFFIX] [--skip SKIP] [--keep] fa_param fb_param f_traj f_coord

GridMAT-MD based automated analysis tool

positional arguments: fa_param GridMAT parameter file for calculating area/lipid

fb_param GridMAT parameter file for calculating thickness

f_traj Trajectory file Formats:xtc trr

f_coord (Structure+mass)db file Format: gro

optional arguments: -h, --help show this help message and exit

-b BTIME, --btime BTIME Starting frame (in ps) Default = None

-e ETIME, --etime ETIME Ending frame (in ps) Default = None

-s SUFFIX, --suffix SUFFIX Binary suffix for the gromacs installation

--skip SKIP Only extract every nr-th frame

--keep Keep output and log files produced by GridMAT. Will take addtional space on drive.

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#Usage note: The perl script provided with this distribution can be used as follows:

perl GridMAT-MD-parallel.pl <param_file> <coord_file> <number_of_frames>

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