gmxhydorder[-f[.xtc/.trr/...]][-n[.ndx]][-s[.tpr/.tpb/...]]. [-o[.xpm[...]]][-or[.out[...]]][-Spect[.out[...]]]
gmxhelixorient[-s[.tpr/.tpb/...]][-f[.xtc/.trr/...]][-n[.ndx]]
gmxhelix[-s[.tpr/.tpb/...]][-n[.ndx]][-f[.xtc/.trr/...]]
gmxhbond[-f[.xtc/.trr/...]][-s[.tpr/.tpb/...]][-n[.ndx]]
gmxh2order[-f[.xtc/.trr/...]][-n[.ndx]][-nm[.ndx]]
gmxgyrate[-f[.xtc/.trr/...]][-s[.tpr/.tpb/...]][-n[.ndx]]
#includefilename在.mdp文件中, 拓扑文件中的这些语句的功能可以通过以下两个选项来模块化:define=-DVARIABLE1-DVARIABLE2
gmxgenrestr[-f[.gro/.g96/...]][-n[.ndx]][-o[.itp]]
gmxgenion[-s[.tpr/.tpb/...]][-n[.ndx]][-o[.gro/.g96/...]]
gmxgenconf[-f[.gro/.g96/...]][-o[.gro/.g96/...]] [-trj[.xtc/.trr/...]][-nice][-nbox] [-dist][-seed][-[no]rot][-[no]shuffle] [-[no]sort][-bloc
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