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
       distances between selected pairs can be plotted with the -pairs option.

       Options -ora, -ort, -oda, -odr and -odt are used for analyzing orientation 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 'a' plot the average over  time  as  a  function  of  restraint.  The
       options  that end on a 't' 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