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gmx-morph - Online in the Cloud

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This is the command gmx-morph that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


gmx-morph - Interpolate linearly between conformations

SYNOPSIS


gmx morph [-f1 [<.gro/.g96/...>]] [-f2 [<.gro/.g96/...>]] [-n [<.ndx>]]
[-o [<.xtc/.trr/...>]] [-or [<.xvg>]] [-[no]w]
[-xvg <enum>] [-ninterm <int>] [-first <real>]
[-last <real>] [-[no]fit]

DESCRIPTION


gmx 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 x_1 to x_2. In general, the coordinates of the intermediate x(i) out of N total
intermediates correspond to:

x(i) = x_1 + (first+(i/(N-1))*(last-first))*(x_2-x_1)

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.

OPTIONS


Options to specify input files:

-f1 [<.gro/.g96/...>] (conf1.gro)
Structure file: gro g96 pdb brk ent esp tpr

-f2 [<.gro/.g96/...>] (conf2.gro)
Structure file: gro g96 pdb brk ent esp tpr

-n [<.ndx>] (index.ndx) (Optional)
Index file

Options to specify output files:

-o [<.xtc/.trr/...>] (interm.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng

-or [<.xvg>] (rms-interm.xvg) (Optional)
xvgr/xmgr file

Other options:

-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files

-xvg <enum>
xvg plot formatting: xmgrace, xmgr, none

-ninterm <int> (11)
Number of intermediates

-first <real> (0)
Corresponds to first generated structure (0 is input x_1, see above)

-last <real> (1)
Corresponds to last generated structure (1 is input x_2, see above)

-[no]fit (yes)
Do a least squares fit of the second to the first structure before interpolating

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