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 recalcu- lated. Additionally running time-averaged and instantaneous distances be- tween 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 op- tions that end on an 'a' plot the average over time as a function of re- straint. 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 2026, GROMACS development team 2026.3 Jun 25, 2026 GMX-NMR(1)
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