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GMX-NMEIG(1)			    GROMACS			  GMX-NMEIG(1)

NAME
       gmx-nmeig - Diagonalize the Hessian for normal mode analysis

SYNOPSIS
	  gmx nmeig [-f	[_.mtx_]] [-s [_.tpr_]]	[-of [_.xvg_]] [-ol [_.xvg_]]
		    [-os [_.xvg_]] [-qc	[_.xvg_]] [-v [_.trr/.cpt/..._]]
		    [-xvg _enum_] [-[no]m] [-first _int_] [-last _int_]
		    [-maxspec _int_] [-T _real_] [-P _real_] [-sigma _int_]
		    [-scale _real_] [-linear_toler _real_] [-[no]constr]
		    [-width _real_]

DESCRIPTION
       gmx  nmeig  calculates  the  eigenvectors/values	of a (Hessian) matrix,
       which can be calculated with gmx	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  and
       eigenvalue  written  as	step  number and timestamp, respectively.  The
       eigenvectors can	be analyzed with gmx anaeig.  An  ensemble  of	struc-
       tures  can be generated from the	eigenvectors with gmx 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 temperature.  The
       total  correction  is  printed on the terminal screen.  The recommended
       way of getting the corrections out is:

       gmx nmeig -s topol.tpr -f nm.mtx	-first 7 -last 10000 -T	300 -qc	[-con-
       str]

       The  -constr option should be used when bond constraints	were used dur-
       ing 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.

       Based  on  a  harmonic analysis of the normal mode frequencies, thermo-
       chemical	properties S0 (Standard	Entropy), Cv (Heat  capacity  at  con-
       stant  volume), Zero-point energy and the internal energy are computed,
       much in the same	manner as popular quantum chemistry programs.

OPTIONS
       Options to specify input	files:

       -f [<.mtx>] (hessian.mtx)
	      Hessian matrix

       -s [<.tpr>] (topol.tpr)
	      Portable xdr run input file

       Options to specify output files:

       -of [<.xvg>] (eigenfreq.xvg)
	      xvgr/xmgr	file

       -ol [<.xvg>] (eigenval.xvg)
	      xvgr/xmgr	file

       -os [<.xvg>] (spectrum.xvg) (Optional)
	      xvgr/xmgr	file

       -qc [<.xvg>] (quant_corr.xvg) (Optional)
	      xvgr/xmgr	file

       -v [<.trr/.cpt/^a|>] (eigenvec.trr)
	      Full precision trajectory: trr cpt tng

       Other options:

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

       -[no]m (yes)
	      Divide elements of Hessian by product of sqrt(mass) of  involved
	      atoms  prior to diagonalization. This should be used for aNormal
	      Modesa analysis

       -first <int> (1)
	      First eigenvector	to write away

       -last <int> (50)
	      Last eigenvector to write	away. -1 is use	all dimensions.

       -maxspec	<int> (4000)
	      Highest frequency	(1/cm) to consider in the spectrum

       -T <real> (298.15)
	      Temperature for computing	entropy, quantum heat capacity and en-
	      thalpy  when using normal	mode calculations to correct classical
	      simulations

       -P <real> (1)
	      Pressure (bar) when computing entropy

       -sigma <int> (1)
	      Number of	symmetric copies used when computing entropy. E.g. for
	      water the	number is 2, for NH3 it	is 3 and for methane it	is 12.

       -scale <real> (1)
	      Factor  to  scale	 frequencies  before computing thermochemistry
	      values

       -linear_toler <real> (1e-05)
	      Tolerance	for determining	whether	a compound is linear as	deter-
	      mined from the ration of the moments inertion Ix/Iy and Ix/Iz.

       -[no]constr (no)
	      If constraints were used in the simulation but not in the	normal
	      mode analysis you	will need to set this for computing the	 quan-
	      tum corrections.

       -width <real> (1)
	      Width  (sigma)  of  the  gaussian	peaks (1/cm) when generating a
	      spectrum

SEE ALSO
       gmx(1)

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

COPYRIGHT
       2020, GROMACS development team

2020.3				 Jul 09, 2020			  GMX-NMEIG(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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