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]]
gmxmake_ndx[-f[.gro/.g96/...]][-n[.ndx[...]]][-o[.ndx]]. nr:group!'name'nrname'splitch'nrEnter:listgroups. 'a':atom'del'nr'splitres'nr'l':listresidues. 't':atomtype|'keep'nr'splitat'nr'h':help. 'r':residue'res'nr'chain'char. Copiedindexgroup2'Protein-H'
gmxmake_edi[-f[.trr/.cpt/...]][-eig[.xvg]][-s[.tpr/.tpb/...]]. [-n[.ndx]][-tar[.gro/.g96/...]][-ori[.gro/.g96/...]]
gmxlie[-f[.edr]][-o[.xvg]][-nice][-b][-e] [-dt][-[no]w][-xvg][-Elj][-Eqq] [-Clj][-Cqq][-ligand]gmx lie基于对非键能的能量分析估算自由能. 程序需要包含Coul-(A-B), LJ-SR(A-
gmxinsert-molecules[-f[.gro/.g96/...]][-ci[.gro/.g96/...]]
微信扫一扫