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Mistake in caculating Benchmark Average


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Mistake in caculating Benchmark Average

There is a basic principal that you cannot average averages. The overall result for the benchmark should be calculated by dviding the sum of the target results by the sum of the baseline results. This is not the same as dividing the sum of the index results by 6. Changing the way this is calculated will give a more mathematically valid way of comparing performance from one host to the other.
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g_bond(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					 g_bond(1)

NAME
g_bond - calculates distances between atoms VERSION 4.5.4-dev-20110404-bc5695c
SYNOPSIS
g_bond -f traj.xtc -n index.ndx -s topol.tpr -o bonds.xvg -l bonds.log -d distance.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -blen real -tol real -[no]aver -[no]averdist
DESCRIPTION
g_bond makes a distribution of bond lengths. If all is well a Gaussian distribution should be made when using a harmonic potential. Bonds are read from a single group in the index file in order i1-j1 i2-j2 through in-jn. -tol gives the half-width of the distribution as a fraction of the bondlength ( -blen). That means, for a bond of 0.2 a tol of 0.1 gives a distribution from 0.18 to 0.22. Option -d plots all the distances as a function of time. This requires a structure file for the atom and residue names in the output. If however the option -averdist is given (as well or separately) the average bond length is plotted instead.
FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input Index file -s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb -o bonds.xvg Output xvgr/xmgr file -l bonds.log Output, Opt. Log file -d distance.xvg Output, Opt. xvgr/xmgr 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 -blen real -1 Bond length. By default length of first bond -tol real 0.1 Half width of distribution as fraction of blen -[no]averyes Average bond length distributions -[no]averdistyes Average distances (turns on -d)
KNOWN PROBLEMS
- It should be possible to get bond information from the topology.
SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_bond(1)

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