# MD file error **URL:** \ **Category:** User discussions\ **Created:** [September 30, 2020, 3:41am UTC](https://gromacs.bioexcel.eu/t/md-file-error/891 "2020-09-30T03:41:54Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![hanguyenxuan](https://avatars.discourse-cdn.com/v4/letter/h/ee59a6/32.png) [@hanguyenxuan](https://gromacs.bioexcel.eu/u/hanguyenxuan)\ **Post date:** [September 30, 2020, 3:41am UTC](https://gromacs.bioexcel.eu/t/md-file-error/891/1 "2020-09-30T03:41:54Z")
GROMACS version: 2020.1 GROMACS modification: Yes/No Hi , there I wanted to pull a ligand out of the protein-ligand complex in the z-axis determined by fast pulling ligand method. But encountered an error during the run like this: ERROR 1 [file md.mdp]: When the maximum distance from a pull group reference atom to other atoms in the group is larger than 0.5 times half the box size a centrally placed atom should be chosen as pbcatom. Pull group 1 is larger than that and does not have a specific atom selected as reference atom. Pull group natoms pbc atom distance at start reference at t=0 1 4516 2258 2 82 4557 0.056 nm 0.056 nm Estimate for the relative computational load of the PME mesh part: 0.31 This run will generate roughly 11 Mb of data My command to run md is as follows: gmx\_mpi\_d grompp -f md.mdp -r npt.gro -c npt.gro -t npt.cpt -p top.top -o md.tpr Previously, I was running NVT and NPT successfully. Here are the options for the md.mdp file. ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/6acb6f2947e41a4e4a10918082d1cda529aa7420.png) The water box designed for the complex is as follows gmx editconf -bt triclinic -c -d 0.8 -f rec.pdb -o rec1.pdb gmx editconf -box 8.316 8.316 12.380 -center 3.808 3.468 3.040 -f rec1.pdb -o rec1.pdb gmx solvate -cp rec1.pdb -cs spc216.gro -p top.top -o rec1.pdb ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/361e3be5fade6996b38a9c43a1d955bc1f5fde47.png) I still don’t understand where the error happened. Can you explain and give a solution for me?. Thanks! ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [September 30, 2020, 9:36am UTC](https://gromacs.bioexcel.eu/t/md-file-error/891/2 "2020-09-30T09:36:51Z")
Hi, you should define a pull-group1-pbcatom (see [http://manual.gromacs.org/current/user-guide/mdp-options.html#mdp-pull-group1-pbcatom](http://manual.gromacs.org/current/user-guide/mdp-options.html#mdp-pull-group1-pbcatom)) in mdp file. That is what the error says. Best regards Alessandra