gmx nmr

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