GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages
GMX-MDMAT(1) GROMACS GMX-MDMAT(1)

gmx-mdmat - Calculate residue contact maps

gmx mdmat [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
          [-mean [<.xpm>]] [-frames [<.xpm>]] [-no [<.xvg>]]
          [-b <time>] [-e <time>] [-dt <time>] [-xvg <enum>]
          [-t <real>] [-nlevels <int>]


gmx mdmat makes distance matrices consisting of the smallest distance between residue pairs. With -frames, these distance matrices can be stored in order to see differences in tertiary structure as a function of time. If you choose your options unwisely, this may generate a large output file. By default, only an averaged matrix over the whole trajectory is output. Also a count of the number of different atomic contacts between residues over the whole trajectory can be made. The output can be processed with gmx xpm2ps to make a PostScript (tm) plot.

Options to specify input files:
-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) (Optional)
Index file

Options to specify output files:

-mean [<.xpm>] (dm.xpm)
X PixMap compatible matrix file
-frames [<.xpm>] (dmf.xpm) (Optional)
X PixMap compatible matrix file
-no [<.xvg>] (num.xvg) (Optional)
xvgr/xmgr file

Other options:

-b <time> (0)
Time of first frame to read from trajectory (default unit ps)
-e <time> (0)
Time of last frame to read from trajectory (default unit ps)
-dt <time> (0)
Only use frame when t MOD dt = first time (default unit ps)
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-t <real> (1.5)
trunc distance
-nlevels <int> (40)
Discretize distance in this number of levels

gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>.

2022, GROMACS development team
January 14, 2022 2021.5

Search for    or go to Top of page |  Section 1 |  Main Index

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with ManDoc.