第二步：使中心分子在盒子内居中, 同时所有其他分子处于盒子内
gmx trjconv -s npt.tpr -f npt.trr -n sdf.ndx -o lignin_cnt.xtc -center -ur compact -pbc mol
Select group for centering时选择中心分子组, Select group for output时选择System组
第三步：按中心分子对轨迹进行叠合, 移除中心分子的转动和平动
gmx trjconv -s npt.tpr -f lignin_cnt.xtc -n sdf.ndx -o lignin_cnt_fit.xtc -fit rot+trans
Select group for least squares fit时选择中心分子组, Select group for output时选择System组。
就是第三步，一直报错，错误如下：
Select group for least squares fit
Group 0 ( System) has 11877 elements
Group 1 ( Other) has 390 elements
Group 2 ( MOL) has 210 elements
Group 3 ( METO) has 180 elements
Group 4 ( Water) has 11487 elements
Group 5 ( SOL) has 11487 elements
Group 6 ( non-Water) has 390 elements
Group 7 ( SI1) has 60 elements
Select a group: 2
Selected 2: 'MOL'
Select group for output
Group 0 ( System) has 11877 elements
Group 1 ( Other) has 390 elements
Group 2 ( MOL) has 210 elements
Group 3 ( METO) has 180 elements
Group 4 ( Water) has 11487 elements
Group 5 ( SOL) has 11487 elements
Group 6 ( non-Water) has 390 elements
Group 7 ( SI1) has 60 elements
Select a group: 7
Selected 7: 'SI1'
Reading frame 0 time 0.000
Precision of lignin_cnt.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
Fatal error:
Index[0] 211 is larger than the number of atoms in the
trajectory file (60). There is a mismatch in the contents
of your -f, -s and/or -n files.