Convert Gromacs v 4.5 trajectory files into MatLab matrix 1.0

%trr2matlab.mby Evan Arthur, University of Michigan, October 2011 Matlab outputs trajectories in a relatively consistent format that isfundamentally challanging and inefficient for Matlab to read directly.This program translates most trr files from recent versions of Gromacsinto binary files that can be read quickly and efficiently into Matlabvia readGmx2Matlab.m.readGmx2Matlab.m is a sibling program that reads the output ofthis program. Currently only coordinates, velocities, and forces areoutput. If I get requests for other outputs (box dimensions, lambdaparameters, etc) I'll fit it in. Requirements: - Gromacs trr trajectory file (GMX trn format) tested on version 4.5 and later - readGmx2Matlab.m (reads the output from this script) - Free RAM: not much. Less than 500 kb for most simulations. - Free Hard Disk: between 1 to 2 times the .trr you input. By default the entire trajectory is copied and reformatted. It takes the output, converts it into a usable format, and then it rewrites the output with useful information. Temp files are removed after all calculations are done, so at most the trajectory is just duplicated in a cleaner format. Limitations: - Broken trr files. If there is a broken frame, it probably should be removed before inputting the trajectory. Inputs: - path to trr file (required, must be first input) - path to output file (optional) if none given, a default name is chosen (such as 'xdata.binary') - 'x' (optional) outputs xyz atomic coordinates - 'v' (optional) outputs xyz of instantaneous velocities - 'f' (optional) outputs xyz of atomic forces Outputs: - xyz data output either by default or if 'x' option is given default name is 'xdata.binary' - velocity data output either by default or if 'v' option is given default name is 'vdata.binary' - force data output either by default or if 'f' option is given default name is 'fdata.binary' Example inputs and outputs: trr2matlab ('traj.trr') outputs all atomic coordinates, velocities, and forces as files 'xdata.binary', 'vdata.binary', and 'fdata.binary' trr2matlab ('traj.trr', 'x', 'f') outputs all atomic coordinates and forces as files 'xdata.binary' and 'fdata.binary' (velocity data is not output) trr2matlab ('traj.trr', 'x') outputs only atomic coordinates as file 'xdata.binary' (velocity and force data are not output) trr2matlab ('traj.trr', 'f', 'proteinA') outputs only atomic forces as file 'proteinA_xdata.binary' (velocity and coordinates data are not output)% readGmx2Matlab.m This program turns the output from trr2matlab.m into matricies for otherprograms to read. These are by default in a ".binary format". The matrixhas introductory code, and the trajectory. There are options to read onlya small portion of the trajectory with a starting frame and ending frameoption. Skipping frames during the reading process (say, to read in everyother frame), is not implimented. If I get requests, I will add it. Requirements: - binary file from trr2matlab.m program - Free RAM: a little more than the size of the binaries being read. 10,000 atoms * 3 axes * 1000 frames = 30 mb (single precision) - Free Hard Disk: none Inputs: - path to binary file (required, must be first input) - start frame (optional) integer, starts reading at this point - end frame (optional) integer, stops reading at this point Outputs: - trajectory matrix this is output as "coodData.trajectory" in the file this is a 3D matrix is made of the trajectory with the format (atom number ; xyz value ; frame number) - information of trajectory coodData.num_atoms has number of atoms coodData.num_frames has number of frames coodData.time_step has the time incriment between frames Example inputs and outputs: [coodData] = readGmx2Matlab('xdata.binary') - makes a 3D matrix (coodData.trajectory) of entire coordinate trajectory [coodData] = readGmx2Matlab('vdata.binary', 1000) - makes a 3D matrix (coodData.trajectory) of velocity trajectory from frames 1 to 1000 [coodData] = readGmx2Matlab('fdata.binary', 1000, 2000) - makes a 3D matrix (coodData.trajectory) of force trajectory from frames 1000 to 2000 [coodData] = readGmx2Matlab('intermedBinary_xdata.binary'); trajectory = coodData.trajectory(:,:,1:2:end); for n = 1:size(trajectory) plot3(trajectory(:,1,n), trajectory(:,2,n), trajectory(:,3,n),'.'); pause(0.2); end - plot out every other frame of trajectory as a 3D figure

Requirements:	No special requirements
Platforms:	Matlab
Keyword:	Introductory,  Matlab,  Matricies,  Matrix,  Options,  Programs,  Proteina,  Proteina Xdatabinary,  Turns
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