g_morph(1) - Linux man page

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 -firstreal -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)