distmat

Description

This tool can be used to calculate:

Average distance matrix: It can be used to calculate average minimum-distance matrix of residues between two atom-groups.

MSF/RMSF in distance-matrix: It can be used to calculate either variance (representing MSF) or standard-deviation (representing RMSF) of distance-matrices.

Contact map: It can be used to calculate contact-frequency map over the trajectory for the residues that are within a minimum distance given by -ct option value.

Fluctuation in second trajectory with reference to average of first trajectory: To calculate fluctuations (MSF - variance or RMSF - std. deviation in distance-matrix) in a trajectory with respect to average distances from another trajectory, use -f traj_for_average.xtc and -f2 traj_for_rmsf.xtc. The averages will be calculated from first trajectory traj_for_average.xtc. Subsequently, variances and deviation will be calculated for traj_for_variance.xtc with respect to previously calculated averages.

Trajectory and pdb for distance-matrix PCA: 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.

Command summary

gmx_clusterByFeatures distmat [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
                              [-n [<.ndx>]] [-f2 [<.xtc/.trr/...>]] [-mean [<.dat>]]
                              [-var [<.dat>]] [-std [<.dat>]] [-cmap [<.dat>]] [-pca [<.xtc>]]
                              [-b <time>] [-e <time>] [-dt <time>] [-ct <real>] [-nt <int>]
                              [-gx <int>] [-gy <int>] [-power <real>]

Options to specify input files to distmat

Option	Default	File type
-f [<.xtc/.trr/…>]	traj.xtc	Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/…>]	topol.tpr	Structure+mass(db): tpr gro g96 pdb brk ent
-n [<.ndx>]	index.ndx	Index file
-f2 [<.xtc/.trr/…>]	traj.xtc	Trajectory: xtc trr cpt gro g96 pdb tng

Options to specify output files to distmat

Option	Default	File type
-mean [<.dat>]	average.dat	Generic data file containing matrix
-var [<.dat>]	variance.dat	Generic data file containing matrix
-std [<.dat>]	stdeviation.dat	Generic data file containing matrix
-cmap [<.dat>]	contact_map.dat	Generic data file containing matrix
-pca [<.xtc>]	pca.xtc	Trajectory format file containing distance-matrix of each frame

Other options to distmat

Option	Default	Description
-b <real>	0	First frame (ps) to read from trajectory
-e <real>	0	Last frame (ps) to read from trajectory
-dt <real>	0	Only use frame when t MOD dt = first time (ps)
-ct <real>	0.4	cut-off distance (nm) for contact map
-nt <int>	All CPU cores	number of threads for multi-threading
-gx <int>	5	Gap between residues along X-axis in distance-matrix for PCA
-gy <int>	1	Gap between residues along Y-axis in distance-matrix for PCA
-power <real>	1	Distances will be raised by this power and then dumped in xtc file

Options to specify input files

-f traj.xtc

Input trajectory file of xtc trr cpt gro g96 pdb or tng format.

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-s topol.tpr

An input structure file of tpr gro g96 or pdb format. It is required if trajectory is given as input.

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-n index.ndx

Two index groups from this file will be prompted for selection. Otherwise, default index groups will be prompted for selection.

Minimum-distance matrix will be calculated between the two selected atom-groups.

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-f2 traj.xtc

Input trajectory file of xtc trr cpt gro g96 pdb or tng format.

Second input trajectory. If this trajectory is provided, fluctuations in this trajectory will be calculated with reference to average-distance matrix of first trajectory.

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Options to specify output files

-mean average.dat

Output file containing average of minimum-distance matrix.

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-var variance.dat

Output file containing variance of minimum-distance matrix over entire trajectory.

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-std stdeviation.dat

Output file containing standard-deviation or RMSF of minimum-distance matrix over entire trajectory.

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-cmap contact_map.dat

Output file containing contact map over entire trajectory. The contact is determined using the threshold distance given by -ct option;

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-pca pca.xtc

Output file containing distance-matrices for each snapshot of the trajectory. This file can be used as input to gmx covar and gmx anaeig for distance matrix PCA.

A dummy pdb file is also dumped to use with gmx covar and gmx anaeig for distance matrix PCA.

Warning

These two outputs are not real trajectory and pdb file. These two files are dumped as a data-container to use with gmx covar and gmx anaeig. For more details, see examples.

Other options

-ct 0.4

cut-off distance (nm) for contact map. Minimum distance below this thershold will be considered to be in contact with each other.

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-nt 4

Number of parallel threads for distance-matrix computation.

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-gx 5

Gap between residues in distance-matrix along X-axis dumped with option -pca for further PCA. This gap reduces the distance-matrix size and subsequently speed-up the PCA performance.

Note

This option ONLY affect output from -pca option.

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-gy 1

Gap between residues in distance-matrix along Y-axis dumped with option -pca for further PCA. This gap reduces the distance-matrix size and subsequently speed-up the PCA performance.

Note

This option ONLY affect output from -pca option.

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-power 1

Distances will be raised by this power and then dumped in xtc file.