## Linux and UNIX Man Pages

Test Your Knowledge in Computers #592
Difficulty: Medium
Suppose we want to sort a huge collection of 1 trillion, 10^12, elements. Doing so with Selection Sort or Insertion Sort would require about n^2 = (10^12)^2 = 10^24 or 1 sextillion comparisons.
True or False?

# g_rmsdist(1) [debian man page]

```g_rmsdist(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c				      g_rmsdist(1)

NAME
g_rmsdist - calculates atom pair distances averaged with power -2, -3 or -6

VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS
g_rmsdist -f traj.xtc -s topol.tpr -n index.ndx -equiv equiv.dat -o distrmsd.xvg -rms rmsdist.xpm -scl rmsscale.xpm -mean rmsmean.xpm -nmr3
nmr3.xpm -nmr6 nmr6.xpm -noe noe.dat -[no]h -[no]version -nice int -b time -e time -dt  time  -[no]w  -xvg  enum  -nlevels  int	-max  real
-[no]sumh -[no]pbc

DESCRIPTION
g_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  g_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.

g_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.:

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.

FILES
-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

-equiv equiv.dat Input, Opt.
Generic data file

-o distrmsd.xvg Output
xvgr/xmgr file

-rms rmsdist.xpm Output, Opt.
X PixMap compatible matrix file

-scl rmsscale.xpm Output, Opt.
X PixMap compatible matrix file

-mean rmsmean.xpm Output, Opt.
X PixMap compatible matrix file

-nmr3 nmr3.xpm Output, Opt.
X PixMap compatible matrix file

-nmr6 nmr6.xpm Output, Opt.
X PixMap compatible matrix file

-noe noe.dat Output, Opt.
Generic data file

OTHER OPTIONS
-[no]hno
Print help info and quit

-[no]versionno
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)

-[no]wno
View output  .xvg,  .xpm,  .eps and  .pdb files

-xvg enum xmgrace
xvg plot formatting:  xmgrace,	xmgr or  none

-nlevels int 40
Discretize rms in  levels

-max real -1
Maximum level in matrices

-[no]sumhyes
average distance over equivalent hydrogens

-[no]pbcyes
Use periodic boundary conditions when computing distances

gromacs(7)

Mon 4 Apr 2011						      g_rmsdist(1)```

## Check Out this Related Man Page

```g_disre(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					g_disre(1)

NAME
g_disre - analyzes distance restraints

VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS
g_disre	-s  topol.tpr  -f  traj.xtc  -ds  drsum.xvg  -da draver.xvg -dn drnum.xvg -dm drmax.xvg -dr restr.xvg -l disres.log -n viol.ndx -q
viol.pdb -c clust.ndx -x matrix.xpm -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -ntop int -maxdr real  -nlevels
int -[no]third

DESCRIPTION
g_disre  computes violations of distance restraints.  If necessary, all protons can be added to a protein molecule using the  g_protonate
program.

The program always computes the instantaneous violations rather than time-averaged, because this analysis is done from  a  trajectory  file
afterwards it does not make sense to use time averaging. However, the time averaged values per restraint are given in the log file.

An index file may be used to select specific restraints for printing.

When the optional  -q flag is given a  .pdb file coloured by the amount of average violations.

When the  -c option is given, an index file will be read containing the frames in your trajectory corresponding to the clusters (defined in
another manner) that you want to analyze. For these clusters the program will compute average violations using the  third  power  averaging
algorithm and print them in the log file.

FILES
-s topol.tpr Input
Run input file: tpr tpb tpa

-f traj.xtc Input
Trajectory: xtc trr trj gro g96 pdb cpt

-ds drsum.xvg Output
xvgr/xmgr file

-da draver.xvg Output
xvgr/xmgr file

-dn drnum.xvg Output
xvgr/xmgr file

-dm drmax.xvg Output
xvgr/xmgr file

-dr restr.xvg Output
xvgr/xmgr file

-l disres.log Output
Log file

-n viol.ndx Input, Opt.
Index file

-q viol.pdb Output, Opt.
Protein data bank file

-c clust.ndx Input, Opt.
Index file

-x matrix.xpm Output, Opt.
X PixMap compatible matrix file

OTHER OPTIONS
-[no]hno
Print help info and quit

-[no]versionno
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)

-[no]wno
View output  .xvg,  .xpm,  .eps and  .pdb files

-xvg enum xmgrace
xvg plot formatting:  xmgrace,	xmgr or  none

-ntop int 0
Number of large violations that are stored in the log file every step

-maxdr real 0
Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data.

-nlevels int 20
Number of levels in the matrix output

-[no]thirdyes
Use inverse third power averaging or linear for matrix output