Fatal error with grompp

User discussions
1

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.

2

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

3

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.

4

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.

5

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.

6

What dimensioned box? What command did you run and what was the error?

Details are important. Give more than you think you need to.

7

I’m facing the similar issue.

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8

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.

9

Thank you! I’ll keep that in mind in future. Fyi, the below-mentioned link solved my issue.