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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.
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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 SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_rmsdist(1)

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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 SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_disre(1)

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