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

6       gmx-nmr  - Analyze nuclear magnetic resonance properties from an energy
7       file
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SYNOPSIS

10          gmx nmr [-f [<.edr>]] [-f2 [<.edr>]] [-s [<.tpr>]] [-viol [<.xvg>]]
11                  [-pairs [<.xvg>]] [-ora [<.xvg>]] [-ort [<.xvg>]]
12                  [-oda [<.xvg>]] [-odr [<.xvg>]] [-odt [<.xvg>]]
13                  [-oten [<.xvg>]] [-b <time>] [-e <time>] [-[no]w]
14                  [-xvg <enum>] [-[no]dp] [-skip <int>] [-[no]aver]
15                  [-[no]orinst] [-[no]ovec]
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DESCRIPTION

18       gmx nmr extracts distance or orientation restraint data from an  energy
19       file. The user is prompted to interactively select the desired terms.
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21       When  the -viol option is set, the time averaged violations are plotted
22       and the running time-averaged and instantaneous sum of  violations  are
23       recalculated. Additionally running time-averaged and instantaneous dis‐
24       tances between selected pairs can be plotted with the -pairs option.
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26       Options -ora, -ort, -oda, -odr and -odt are used for analyzing orienta‐
27       tion  restraint  data.  The first two options plot the orientation, the
28       last three the deviations of the  orientations  from  the  experimental
29       values.  The options that end on an ‘a’ plot the average over time as a
30       function of restraint. The options that end on a ‘t’  prompt  the  user
31       for  restraint  label  numbers and plot the data as a function of time.
32       Option -odr plots the RMS deviation as a function of  restraint.   When
33       the  run  used time or ensemble averaged orientation restraints, option
34       -orinst can be used to analyse the instantaneous, not ensemble-averaged
35       orientations and deviations instead of the time and ensemble averages.
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37       Option  -oten  plots  the eigenvalues of the molecular order tensor for
38       each orientation restraint  experiment.  With  option  -ovec  also  the
39       eigenvectors are plotted.
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OPTIONS

42       Options to specify input files:
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44       -f [<.edr>] (ener.edr)
45              Energy file
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47       -f2 [<.edr>] (ener.edr) (Optional)
48              Energy file
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50       -s [<.tpr>] (topol.tpr) (Optional)
51              Portable xdr run input file
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53       Options to specify output files:
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55       -viol [<.xvg>] (violaver.xvg) (Optional)
56              xvgr/xmgr file
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58       -pairs [<.xvg>] (pairs.xvg) (Optional)
59              xvgr/xmgr file
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61       -ora [<.xvg>] (orienta.xvg) (Optional)
62              xvgr/xmgr file
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64       -ort [<.xvg>] (orientt.xvg) (Optional)
65              xvgr/xmgr file
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67       -oda [<.xvg>] (orideva.xvg) (Optional)
68              xvgr/xmgr file
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70       -odr [<.xvg>] (oridevr.xvg) (Optional)
71              xvgr/xmgr file
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73       -odt [<.xvg>] (oridevt.xvg) (Optional)
74              xvgr/xmgr file
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76       -oten [<.xvg>] (oriten.xvg) (Optional)
77              xvgr/xmgr file
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79       Other options:
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81       -b <time> (0)
82              Time of first frame to read from trajectory (default unit ps)
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84       -e <time> (0)
85              Time of last frame to read from trajectory (default unit ps)
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87       -[no]w (no)
88              View output .xvg, .xpm, .eps and .pdb files
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90       -xvg <enum> (xmgrace)
91              xvg plot formatting: xmgrace, xmgr, none
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93       -[no]dp (no)
94              Print energies in high precision
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96       -skip <int> (0)
97              Skip number of frames between data points
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99       -[no]aver (no)
100              Also  print  the  exact  average  and  rmsd stored in the energy
101              frames (only when 1 term is requested)
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103       -[no]orinst (no)
104              Analyse instantaneous orientation data
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106       -[no]ovec (no)
107              Also plot the eigenvectors with -oten
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SEE ALSO

110       gmx(1)
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112       More    information    about    GROMACS    is    available    at     <‐
113       http://www.gromacs.org/>.
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116       2019, GROMACS development team
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1212019.2                           Apr 16, 2019                       GMX-NMR(1)
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