This tool is moved to gmx_clusterByFeatures as sub-command distmat.

gmx_clusterByFeatures is easy to install by one command: sudo pip3 install gmx-clusterByFeatures. distmat command is same as g_distMat. HELP and USAGE for distmat is provided in this link. Moreover, gmx_clusterByFeatures include matplot, which can be used to plot the data obtained from distmat.

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g_distMat

About

This tool is similar to gromacs tool g_mdmat. It calculates average minimum-distance matrix and other related matrices between two atom-groups from molecular dynamics trajectory (GROMACS, NAMD or AMBER).

This tool might be helpful to analyze binding interface in protein-protein, protein-ligand or other type of bio-molecular complexes.

Features

• Average minimum residues-distance matrix between two atom-groups that may be identical or different.
• Related Standard deviation and variance Matrix.
• Contact-map (fraction of contacts over entire trajectory) for the given distance cut-off.
• Parallel Calculation -- multi-threading to use more than one core of the multi-core processor.
• Compare fluctuations in two different trajectory

Requirements

Gromacs versions supported: 4.5.x, 4.6.x, 5.0.x, 5.1.x and 2016.x

To compile and install, GROMACS libraries libgmx.a(.so) (v4.5.x/v4.6.x) or libgromacs.a(.so) (v5.0.x/v5.1.x/v2016.x) are required.

Download

git clone https://github.com/rjdkmr/g_distMat

Installation

cd g_distMat
mkdir build
cd build
cmake ..  -DGMX_PATH=/opt/gromacs -DCMAKE_INSTALL_PREFIX=/opt/g_distMat
make
make install

Directory /opt/gromacs should contains include and lib directories.

If fftw library libfftw3f.so or libfftw3f.a are not present in standard locations:

-DFFTW_LIB=/path/to/fftw3/lib

Usage

g_distMat -h

Description

It calculates average minimum-distance matrix of residues between two atom-groups. Simultaneously, it calculates variance and standard-deviation matrices. Also, it calculates contact-frequency map over the trajectory for the residues that are within a minimum distance given by "-ct" option value.

To speed up the calculation, it uses all available cores of the CPU using multi-threading. Number of threads/cores could be change by "-nt" option.

To calculate distance variances or deviation (fluctuations) in a trajectory with respect to average distances from another trajectory, use [-f traj_for_average.xtc]
and [-f2 traj_for_variance.xtc]. The averages will be calculated from "traj_for_average.xtc". Subsequently, variances and deviation will be calculated for "traj_for_variance.xtc" with respect to previosly calculated averages.

Options

Option     Filename  Type         Description
------------------------------------------------------------
  -f       traj.xtc  Input        Trajectory: xtc trr trj gro g96 pdb cpt
  -s      topol.tpr  Input        Structure+mass(db): tpr tpb tpa gro g96 pdb
  -n      index.ndx  Input, Opt.  Index file
 -f2       traj.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-mean   average.dat  Output       Generic data file
-var   variance.dat  Output, Opt. Generic data file
-std stdeviation.dat  Output, Opt. Generic data file
-cmap contact_map.dat  Output, Opt. Generic data file

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   yes     Print help info and quit
-[no]version bool   no      Print version info and quit
-nice        int    19      Set the nicelevel
-b           time   0       First frame (ps) to read from trajectory
-e           time   0       Last frame (ps) to read from trajectory
-dt          time   0       Only use frame when t MOD dt = first time (ps)
-ct          real   0.4     cut-off distance (nm) for contact map
-nt          int    8       number of threads for multi-threading

Ouput

Output files contain values in two-dimensional matrix format. This type of file could be visualized with gnuplot as shown in following example:

gnuplot> plot 'contact_map.dat' matrix with image

Color of this plot could be easily changed as per the gnuplot manual.