我在用gromacs生成grid.cube文件时，
第一步：以所有要研究的分子为中心分子建一个组，以体系中所有水建一个组，用这两个组计算sdf。
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_mpi trjconv -s md0.tpr -f md0.trr -n sdf.ndx -o md0_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_mpi trjconv -s md0.tpr -f md0_cnt.xtc -n sdf.ndx -o md0_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 output
Group 0 ( System) has 16401 elements
Group 1 ( Other) has 16401 elements
Group 2 ( P44) has 10600 elements
Group 3 ( cf3) has 1400 elements
Group 4 ( SPC) has 4401 elements
Select a group: 4
Selected 4: 'SPC'
Reading frame 0 time 0.000
Precision of md2_cnt.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)
Back Off! I just backed up md2_cnt_fit.xtc to ./#md2_cnt_fit.xtc.1#
-------------------------------------------------------
Program trjconv_mpi_d, VERSION 4.6.3
Source code file: /public/software/Gromacs/gromacs-4.6.3/src/tools/gmx_trjconv.c, line: 1312
Fatal error:
Index[0] 12001 is larger than the number of atoms in the
trajectory file (4401). There is a mismatch in the contents
of your -f, -s and/or -n files.