# About fatal error **URL:** \ **Category:** User discussions\ **Created:** [January 26, 2021, 3:27pm UTC](https://gromacs.bioexcel.eu/t/about-fatal-error/1486 "2021-01-26T15:27:16Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![torquato](https://avatars.discourse-cdn.com/v4/letter/t/8baadc/32.png) [@torquato](https://gromacs.bioexcel.eu/u/torquato)\ **Post date:** [January 26, 2021, 3:27pm UTC](https://gromacs.bioexcel.eu/t/about-fatal-error/1486/1 "2021-01-26T15:27:16Z")
GROMACS version:2021-rc1 GROMACS modification: No How can I get over this problem ? gmx grompp -f md\_pull.mdp -c npt.gro -p topol.top -r npt.gro -n index.ndx -t npt.cpt -o pull.tpr Ignoring obsolete mdp entry ‘title’ Ignoring obsolete mdp entry ‘optimize\_fft’ Ignoring obsolete mdp entry ‘ns\_type’ Replacing old mdp entry ‘nstxtcout’ by ‘nstxout-compressed’ Setting the LD random seed to -1258291201 Generated 2145 of the 2145 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2145 of the 2145 1-4 parameter combinations Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_E’ turning H bonds into constraints… Excluding 3 bonded neighbours molecule type ‘Protein\_chain\_I’ turning H bonds into constraints… Excluding 2 bonded neighbours molecule type ‘SOL’ turning H bonds into constraints… Excluding 1 bonded neighbours molecule type ‘NA’ turning H bonds into constraints… Excluding 1 bonded neighbours molecule type ‘CL’ turning H bonds into constraints… Pull group 1 ‘Chain\_E’ has 3564 atoms Pull group 2 ‘Chain\_I’ has 861 atoms Number of degrees of freedom in T-Coupling group Protein is 9552.64 Number of degrees of freedom in T-Coupling group non-Protein is 70181.36 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 310 K Calculated rlist for 1x1 atom pair-list as 1.433 nm, buffer size 0.033 nm Set rlist, assuming 4x4 atom pair-list, to 1.400 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Reading Coordinates, Velocities and Box size from old trajectory Will read whole trajectory Last frame -1 time 100.000 Using frame at t = 100 ps Starting time for run is 0 ps Calculating fourier grid dimensions for X Y Z Using a fourier grid of 56x40x100, spacing 0.117 0.109 0.119 ERROR 1 [file md\_pull.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 3564 1782 2 861 3389 0.165 nm 0.165 nm Estimate for the relative computational load of the PME mesh part: 0.13 This run will generate roughly 319 Mb of data * * * Program: gmx grompp, version 2021-rc1-UNCHECKED Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2382) ---
**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:** [January 26, 2021, 3:36pm UTC](https://gromacs.bioexcel.eu/t/about-fatal-error/1486/2 "2021-01-26T15:36:41Z")
Hi, you can define `pull-group1-pbcatom` in the mdp file, it should solve the problem [https://manual.gromacs.org/current/user-guide/mdp-options.html#mdp-pull-group1-pbcatom](https://manual.gromacs.org/current/user-guide/mdp-options.html#mdp-pull-group1-pbcatom) Alessandra