1GMX-NMR(1) GROMACS GMX-NMR(1)
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6 gmx-nmr - Analyze nuclear magnetic resonance properties from an energy
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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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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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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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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 2020, GROMACS development team
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1212019.6 Feb 28, 2020 GMX-NMR(1)