Poster of Linux kernelThe best gift for a Linux geek
g_morph

g_morph

Section: GROMACS suite, VERSION 4.5 (1) Updated: Thu 26 Aug 2010
Local index Up
 

NAME

g_morph - linear interpolation of conformations

VERSION 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]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 what group RMS is computed from.  

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/>.


 

Index

NAME
SYNOPSIS
DESCRIPTION
FILES
OTHER OPTIONS
SEE ALSO

This document was created by man2html, using the manual pages.
Time: 21:13:24 GMT, April 16, 2011