gmxprotonate[-s[.tpr/.tpb/...]][-f[.xtc/.trr/...]][-n[.ndx]]
gmxprincipal[-f[.xtc/.trr/...]][-s[.tpr/.tpb/...]][-n[.ndx]]
gmxpotential[-f[.xtc/.trr/...]][-n[.ndx]][-s[.tpr/.tpb/...]]
gmxpolystat[-s[.tpr/.tpb/...]][-f[.xtc/.trr/...]][-n[.ndx]]
gmxpme_error[-s[.tpr/.tpb/...`]][-o[.out`]][-so[.tpr/.tpb/...`]]
gmxpdb2gmx[-f[.gro/.g96/...]][-o[.gro/.g96/...]][-p[.top]]. [-[no]inter][-[no]ss][-[no]ter][-[no]lys][-[no]arg]. [-dist][-[no]una][-[no]ignh][-[no]missing][-[no]v]
[-s[.tpr/.tpb/...]][-o[.xvg]][-od[.xvg]][-ob[.pdb]]
gmxnmtraj[-s[.tpr/.tpb/...]][-v[.trr/.cpt/...]] [-o[.xtc/.trr/...]][-nice][-eignr] [-phases][-temp][-amplitude] [-nframes]gmx nmtraj根据特征向量产生虚拟的轨
gmxnmens[-v[.trr/.cpt/...]][-e[.xvg]][-s[.tpr/.tpb/...]]
gmxnmeig[-f[.mtx]][-s[.tpr/.tpb/...]][-of[.xvg]][-ol[.xvg]]
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