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GMX-NMR(1)			    GROMACS			    GMX-NMR(1)

NAME
       gmx-nmr	- Analyze nuclear magnetic resonance properties	from an	energy
       file

SYNOPSIS
	  gmx nmr [-f [_.edr_]]	[-f2 [_.edr_]] [-s [_.tpr_]] [-viol [_.xvg_]]
		  [-pairs [_.xvg_]] [-ora [_.xvg_]] [-ort [_.xvg_]]
		  [-oda	[_.xvg_]] [-odr	[_.xvg_]] [-odt	[_.xvg_]]
		  [-oten [_.xvg_]] [-b _time_] [-e _time_] [-[no]w]
		  [-xvg	_enum_]	[-[no]dp] [-skip _int_]	[-[no]aver]
		  [-[no]orinst]	[-[no]ovec]

DESCRIPTION
       gmx nmr extracts	distance or orientation	restraint data from an	energy
       file. The user is prompted to interactively select the desired terms.

       When  the -viol option is set, the time averaged	violations are plotted
       and the running time-averaged and instantaneous sum of  violations  are
       recalculated. Additionally running time-averaged	and instantaneous dis-
       tances between selected pairs can be plotted with the -pairs option.

       Options -ora, -ort, -oda, -odr and -odt are used	for analyzing orienta-
       tion  restraint	data.  The first two options plot the orientation, the
       last three the deviations of the	 orientations  from  the  experimental
       values.	The options that end on	an aaa plot the	average	over time as a
       function	of restraint. The options that end on a	ata  prompt  the  user
       for  restraint  label  numbers and plot the data	as a function of time.
       Option -odr plots the RMS deviation as a	function of  restraint.	  When
       the  run	 used time or ensemble averaged	orientation restraints,	option
       -orinst can be used to analyse the instantaneous, not ensemble-averaged
       orientations and	deviations instead of the time and ensemble averages.

       Option  -oten  plots  the eigenvalues of	the molecular order tensor for
       each orientation	restraint  experiment.	With  option  -ovec  also  the
       eigenvectors are	plotted.

OPTIONS
       Options to specify input	files:

       -f [<.edr>] (ener.edr)
	      Energy file

       -f2 [<.edr>] (ener.edr) (Optional)
	      Energy file

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

       Options to specify output files:

       -viol [<.xvg>] (violaver.xvg) (Optional)
	      xvgr/xmgr	file

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

       -ora [<.xvg>] (orienta.xvg) (Optional)
	      xvgr/xmgr	file

       -ort [<.xvg>] (orientt.xvg) (Optional)
	      xvgr/xmgr	file

       -oda [<.xvg>] (orideva.xvg) (Optional)
	      xvgr/xmgr	file

       -odr [<.xvg>] (oridevr.xvg) (Optional)
	      xvgr/xmgr	file

       -odt [<.xvg>] (oridevt.xvg) (Optional)
	      xvgr/xmgr	file

       -oten [<.xvg>] (oriten.xvg) (Optional)
	      xvgr/xmgr	file

       Other options:

       -b <time> (0)
	      Time of first frame to read from trajectory (default unit	ps)

       -e <time> (0)
	      Time of last frame to read from trajectory (default unit ps)

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

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

       -[no]dp (no)
	      Print energies in	high precision

       -skip <int> (0)
	      Skip number of frames between data points

       -[no]aver (no)
	      Also  print  the	exact  average	and  rmsd stored in the	energy
	      frames (only when	1 term is requested)

       -[no]orinst (no)
	      Analyse instantaneous orientation	data

       -[no]ovec (no)
	      Also plot	the eigenvectors with -oten

SEE ALSO
       gmx(1)

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

COPYRIGHT
       2020, GROMACS development team

2020.4				 Oct 06, 2020			    GMX-NMR(1)

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

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