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g_morph
Langue: en
Version: 371386 (fedora - 01/12/10)
Section: 1 (Commandes utilisateur)
NAME
g_morph - linear interpolation of conformationsVERSION 4.5
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]fitDESCRIPTION
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 what group RMS is computed from.
FILES
-f1 conf1.gro InputStructure 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]hnoPrint 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/>.
Contenus ©2006-2024 Benjamin Poulain
Design ©2006-2024 Maxime Vantorre