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


Manual Reference Pages  -  GMX-RMSDIST (1)

NAME

gmx-rmsdist - Calculate atom pair distances averaged with power -2, -3 or -6

CONTENTS

Synopsis
Description
Options
See Also

SYNOPSIS

gmx rmsdist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.tpb/...>]]
[-n [<.ndx>]] [-equiv [<.dat>]] [-o [<.xvg>]]
[-rms [<.xpm>]] [-scl [<.xpm>]] [-mean [<.xpm>]]
[-nmr3 [<.xpm>]] [-nmr6 [<.xpm>]] [-noe [<.dat>]]
[-nice <int>] [-b <time>] [-e <time>] [-dt <time>]
[-[no]w] [-xvg <enum>] [-nlevels <int>] [-max <real>]
[-[no]sumh] [-[no]pbc]

DESCRIPTION

gmx rmsdist computes the root mean square deviation of atom distances, which has the advantage that no fit is needed like in standard RMS deviation as computed by gmx rms. The reference structure is taken from the structure file. The RMSD at time t is calculated as the RMS of the differences in distance between atom-pairs in the reference structure and the structure at time t.

gmx rmsdist can also produce matrices of the rms distances, rms distances scaled with the mean distance and the mean distances and matrices with NMR averaged distances (1/r3 and 1/r6 averaging). Finally, lists of atom pairs with 1/r3 and 1/r6 averaged distance below the maximum distance (-max, which will default to 0.6 in this case) can be generated, by default averaging over equivalent hydrogens (all triplets of hydrogens named *[123]). Additionally a list of equivalent atoms can be supplied (-equiv), each line containing a set of equivalent atoms specified as residue number and name and atom name; e.g.:

HB* 3 SER HB1 3 SER HB2

Residue and atom names must exactly match those in the structure file, including case. Specifying non-sequential atoms is undefined.

OPTIONS

Options to specify input and output files:

-f [<.xtc/.trr/...>] (traj.xtc) (Input)
Trajectory: xtc trr cpt trj gro g96 pdb tng

-s [<.tpr/.tpb/...>] (topol.tpr) (Input)
Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

-n [<.ndx>] (index.ndx) (Input, Optional)
Index file

-equiv [<.dat>] (equiv.dat) (Input, Optional)
Generic data file

-o [<.xvg>] (distrmsd.xvg) (Output)
xvgr/xmgr file

-rms [<.xpm>] (rmsdist.xpm) (Output, Optional)
X PixMap compatible matrix file

-scl [<.xpm>] (rmsscale.xpm) (Output, Optional)
X PixMap compatible matrix file

-mean [<.xpm>] (rmsmean.xpm) (Output, Optional)
X PixMap compatible matrix file

-nmr3 [<.xpm>] (nmr3.xpm) (Output, Optional)
X PixMap compatible matrix file

-nmr6 [<.xpm>] (nmr6.xpm) (Output, Optional)
X PixMap compatible matrix file

-noe [<.dat>] (noe.dat) (Output, Optional)
Generic data file

Other options:

-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)

-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files

-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none

-nlevels <int> (40)
Discretize RMS in this number of levels

-max <real> (-1)
Maximum level in matrices

-[no]sumh (yes)
Average distance over equivalent hydrogens

-[no]pbc (yes)
Use periodic boundary conditions when computing distances

SEE ALSO

gromacs(7)

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

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


VERSION 5.0.6 GMX-RMSDIST (1)

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with manServer 1.07.