[-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]]
gmxmsd[-f[.xtc/.trr/...]][-s[.tpr/.tpb/...]][-n[.ndx]]
gmxmorph[-f1[.gro/.g96/...]][-f2[.gro/.g96/...]] [-o[.xtc/.trr/...]][-or[.xvg]][-n[.ndx]][-nice] [-[no]w][-xvg][-ninterm][-first] [-last][-[no]f
gmxmk_angndx[-s[.tpr/.tpb/...]][-n[.ndx]][-nice] [-type][-[no]hyd][-hq]gmx mk_angndx命令用于创建索引文件, 以计算角度分布等. 它需要使用一个运行输入文件(.tpx)来获得键角, 二面角等的信息.输入/输出文件
gmxmindist[-f[.xtc/.trr/...]][-s[.tpr/.tpb/...]][-n[.ndx]]
gmxmdrun[-s[.tpr/.tpb/...]][-o[.trr/.cpt/...]][-x[.xtc/.tng]]. [-cpi[.cpt]][-cpo[.cpt]][-c[.gro/.g96/...]]. [-e[.edr]][-g[.log]][-dhdl[.xvg]][-field[.xvg]]. [-table[.xvg]][-tabletf[.xvg]][-tablep[.xvg]]. [-tableb[.xvg]][-rerun[.xtc/.trr/...]][-tpi[.xvg]]. [-tpid[.xvg]][-ei[.edi]][-eo[.xvg]][-devout[.xvg]]. [-runav[.xvg]][-px[.xvg]][-pf[.xvg]][-ro[.xvg]]. [-ra[.log]][-rs[.log]][-rt[.log]][-mtx[.mtx]]. [-dn[.ndx]][-multidir[. [...]]][-membed[.dat]]. [-mp[.top]][-mn[.ndx]][-if[.xvg]][-swap[.xvg]]. [-nice][-deffnm][-xvg][-dd]. [-ddorder][-npme][-nt][-ntmpi]. [-ntomp][-ntomp_pme][-pin][-pinoffset]. [-pinstride][-gpu_id][-[no]ddcheck][-rdd]. [-rcon][-dlb][-dds][-gcom]. [-nb][-nstlist][-[no]tunepme][-[no]testverlet]. [-[no]v][-[no]compact][-[no]seppot][-pforce]. [-[no]reprod][-cpt][-[no]cpnum][-[no]append]. [-nsteps][-maxh][-multi][-replex]
gmxmdmat[-f[.xtc/.trr/...]][-s[.tpr/.tpb/...]][-n[.ndx]]
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