Provided by: gromacs-data_2019.3-2_all bug

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

       2019, GROMACS development team