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UNIX for Dummies Questions & Answers
ps command
Post 302644575 by muffle on Tuesday 22nd of May 2012 06:58:00 AM
05-22-2012
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LEARN ABOUT DEBIAN
g_morph
g_morph(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_morph(1) NAME
g_morph - linear interpolation of conformations VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_morph -f1 conf1.gro -f2 conf2.gro -o interm.xtc -or rms-interm.xvg -n index.ndx -[no]h -[no]version -nice int -[no]w -xvg enum -ninterm int -first real -last real -[no]fit DESCRIPTION
g_morph does a linear interpolation of conformations in order to create intermediates. Of course these are completely unphysical, but that you may try to justify yourself. Output is in the form of a generic trajectory. The number of intermediates can be controlled with the -ninterm flag. The first and last flag correspond to the way of interpolating: 0 corresponds to input structure 1 while 1 corresponds to input structure 2. If you specify -first 0 or -last 1 extrapolation will be on the path from input structure x1 to x2. In general, the coordinates of the intermediate x(i) out of N total intermidates correspond to: x(i) = x1 + (first+(i/(N-1))*(last-first))*(x2-x1) Finally the RMSD with respect to both input structures can be computed if explicitly selected ( -or option). In that case, an index file may be read to select the group from which the RMS is computed. FILES
-f1 conf1.gro Input Structure file: gro g96 pdb tpr etc. -f2 conf2.gro Input Structure file: gro g96 pdb tpr etc. -o interm.xtc Output Trajectory: xtc trr trj gro g96 pdb cpt -or rms-interm.xvg Output, Opt. xvgr/xmgr file -n index.ndx Input, Opt. Index file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 0 Set the nicelevel -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -ninterm int 11 Number of intermediates -first real 0 Corresponds to first generated structure (0 is input x0, see above) -last real 1 Corresponds to last generated structure (1 is input x1, see above) -[no]fityes Do a least squares fit of the second to the first structure before interpolating SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_morph(1)