# Fatal error with grompp **URL:** \ **Category:** User discussions\ **Created:** [September 30, 2020, 12:16pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/893 "2020-09-30T12:16:13Z")\ **Posts on this page:** 9\ **Page:** 1
**Author:** ![Tarun237](https://avatars.discourse-cdn.com/v4/letter/t/898d66/32.png) [@Tarun237](https://gromacs.bioexcel.eu/u/Tarun237)\ **Post date:** [September 30, 2020, 12:16pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/893/1 "2020-09-30T12:16:13Z")
GROMACS version: 2020.3 GROMACS modification: Yes/No I’m a beginner trying to do membrane bound protein simulation. Upon giving the command “ **gmx grompp -f em\_inflategro.mdp -c system\_inflated.gro -p topol.top -r system\_inflated.gro -o system\_inflated\_em.tpr** ” I get the following error ERROR 1 [file topol.top, line 76514]: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. I checked my topol.top file (line 76514) which is actually the last line in the file stating the number of POPC molecules in [molecules] section. I have also tried resizing the simulation box but nothing seems to work. Please guide me through it. Thank you. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [September 30, 2020, 7:03pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/893/2 "2020-09-30T19:03:54Z")
The topology line is irrelevant and honestly somewhat confusing. It just means `grompp` has finished parsing your system and has found an issue, though one that has nothing to do with the topology and everything to do with the coordinates. See [http://manual.gromacs.org/current/user-guide/run-time-errors.html#the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diagonal-element-increase-the-box-size-or-decrease-rlist](http://manual.gromacs.org/current/user-guide/run-time-errors.html#the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diagonal-element-increase-the-box-size-or-decrease-rlist) ---
**Author:** ![Tarun237](https://avatars.discourse-cdn.com/v4/letter/t/898d66/32.png) [@Tarun237](https://gromacs.bioexcel.eu/u/Tarun237)\ **Post date:** [October 2, 2020, 8:36am UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/893/3 "2020-10-02T08:36:20Z")
I have already tried increasing the size of the simulation box but it still doesn’t work. Can you please help me in understanding whether the topology file should include all the details (.itp) of the lipid bilayer or just the number of lipid molecules in the molecules section ? I have a feeling something is wrong here in my topology file. ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [October 2, 2020, 1:42pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/893/4 "2020-10-02T13:42:36Z")
The topology has to be a full description of the molecule definitions and associated parameters. Again, the error is not related to the topology; you would see other problems coming from `grompp` if there were. ---
**Author:** ![Tarun237](https://avatars.discourse-cdn.com/v4/letter/t/898d66/32.png) [@Tarun237](https://gromacs.bioexcel.eu/u/Tarun237)\ **Post date:** [October 2, 2020, 2:32pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/893/5 "2020-10-02T14:32:38Z")
Thanks for your guidance, but I’m still not clear as to what needs to be done to resolve this issue. Resizing the box doesn’t work, I tried creating a new box too but nothing fruitful came out of it. ---
**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\ **Post date:** [October 4, 2020, 11:13pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/893/6 "2020-10-04T23:13:14Z")
What dimensioned box? What command did you run and what was the error? Details are important. Give more than you think you need to. ---
**Author:** ![iy55](https://avatars.discourse-cdn.com/v4/letter/i/87869e/32.png) [@iy55](https://gromacs.bioexcel.eu/u/iy55)\ **Post date:** [October 26, 2020, 4:23pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/893/7 "2020-10-26T16:23:55Z")
I’m facing the similar issue. ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/1X/8b60865c77e6e5e793026d6b9b8ba8844576dc4f.png) ---
**Author:** ![Dr\_DBW](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/dr_dbw/32/42_2.png) [@Dr\_DBW](https://gromacs.bioexcel.eu/u/Dr_DBW)\ **Post date:** [October 26, 2020, 9:45pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/893/8 "2020-10-26T21:45:23Z")
> **[Common errors when using GROMACS — GROMACS 2020.4 documentation](http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html?the-cut-off-length-is-longer-than-half-the-shortest-box-vector-or-longer-than-the-smallest-box-diagonal-element-increase-the-box-size-or-decrease-rlist)** It is best for you to start a new topic for your question(s), rather than attaching it to the end of someone else’s. ---
**Author:** ![iy55](https://avatars.discourse-cdn.com/v4/letter/i/87869e/32.png) [@iy55](https://gromacs.bioexcel.eu/u/iy55)\ **Post date:** [October 28, 2020, 2:07am UTC](https://gromacs.bioexcel.eu/t/fatal-error-with-grompp/893/9 "2020-10-28T02:07:32Z")
Thank you! I’ll keep that in mind in future. Fyi, the below-mentioned link solved my issue. > **[gmx insert-molecules — GROMACS 2018 documentation](http://manual.gromacs.org/documentation/2018/onlinehelp/gmx-insert-molecules.html)**