debian man page for g_nmeig

g_nmeig(1)					 GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c					g_nmeig(1)

NAME
       g_nmeig - diagonalizes the Hessian

       VERSION 4.5.4-dev-20110404-bc5695c

SYNOPSIS
       g_nmeig	-f  hessian.mtx  -s  topol.tpr -of eigenfreq.xvg -ol eigenval.xvg -qc quant_corr.xvg -v eigenvec.trr -[no]h -[no]version -nice int
       -xvg enum -[no]m -first int -last int -T real -[no]constr

DESCRIPTION
	g_nmeig calculates the eigenvectors/values of a (Hessian) matrix, which can be calculated with	mdrun.	The eigenvectors are written to  a
       trajectory  file  (  -v).   The	structure is written first with t=0. The eigenvectors are written as frames with the eigenvector number as
       timestamp.  The eigenvectors can be analyzed with  g_anaeig.  An ensemble of structures can  be	generated  from  the  eigenvectors  with
       g_nmens.  When  mass weighting is used, the generated eigenvectors will be scaled back to plain Cartesian coordinates before generating the
       output. In this case, they will no longer be exactly orthogonal in the standard Cartesian norm, but in the mass-weighted  norm  they  would
       be.

       This  program  can  be  optionally  used  to  compute quantum corrections to heat capacity and enthalpy by providing an extra file argument
       -qcorr. See the GROMACS manual, Chapter 1, for details. The result includes subtracting a harmonic degree of freedom at the given  tempera-
       ture.  The total correction is printed on the terminal screen.  The recommended way of getting the corrections out is:

	g_nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-constr]

       The   -constr  option  should be used when bond constraints were used during the simulation  for all the covalent bonds. If this is not the
       case, you need to analyze the  quant_corr.xvg file yourself.

       To make things more flexible, the program can also take virtual sites into account  when  computing  quantum  corrections.  When  selecting
       -constr	and    -qc, the  -begin and  -end options will be set automatically as well.  Again, if you think you know it better, please check
       the  eigenfreq.xvg output.

FILES
       -f hessian.mtx Input
	Hessian matrix

       -s topol.tpr Input
	Run input file: tpr tpb tpa

       -of eigenfreq.xvg Output
	xvgr/xmgr file

       -ol eigenval.xvg Output
	xvgr/xmgr file

       -qc quant_corr.xvg Output, Opt.
	xvgr/xmgr file

       -v eigenvec.trr Output
	Full precision trajectory: trr trj cpt

OTHER OPTIONS
       -[no]hno
	Print help info and quit

       -[no]versionno
	Print version info and quit

       -nice int 19
	Set the nicelevel

       -xvg enum xmgrace
	xvg plot formatting:  xmgrace,	xmgr or  none

       -[no]myes
	Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be	used  for  'Normal  Modes'
       analysis

       -first int 1
	First eigenvector to write away

       -last int 50
	Last eigenvector to write away

       -T real 298.15
	Temperature for computing quantum heat capacity and enthalpy when using normal mode calculations to correct classical simulations

       -[no]constrno
	If  constraints were used in the simulation but not in the normal mode analysis (this is the recommended way of doing it) you will need to
       set this for computing the quantum corrections.

SEE ALSO
       gromacs(7)

       More information about GROMACS is available at <http://www.gromacs.org/>.

								  Mon 4 Apr 2011							g_nmeig(1)