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>]
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 |
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 |
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.
-s topol.tpr
¶
An input structure file of tpr
gro
g96
or pdb
format. It is required
if trajectory is given as input.
-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.
-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.
Options to specify output files¶
-mean average.dat
¶
Output file containing average of minimum-distance matrix.
-var variance.dat
¶
Output file containing variance of minimum-distance matrix over entire trajectory.
-std stdeviation.dat
¶
Output file containing standard-deviation or RMSF of minimum-distance matrix over entire trajectory.
-cmap contact_map.dat
¶
Output file containing contact map over entire trajectory. The contact is determined
using the threshold distance given by -ct
option;
-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.
-nt 4
¶
Number of parallel threads for distance-matrix computation.
-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.
-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.
-power 1
¶
Distances will be raised by this power and then dumped in xtc file.