How to fix the error by DFT calculation for charged molecule?

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

I drew a charged molecule by getting rid of one hydrogen ion from acetic acid using Avogrado program.
Then I put this .pdb file to Gaussview 6 and assigned “-1” charge as a global charge and save it as .gjf file.
The settings were:
Method: Ground State, DFT, Default Spin, B3LYP
Basis Set: 6-31G, +, (d,p)
Charge: -1, Spin: Singlet

I submitted it (sbatch .sh file) on swarm by using “g16 acetic_acid_ion.gjf”
(Question: is this .gjf file incorrect?)

acetic_acid_ion.gjf
acetic_acid_ion.gjf689×719 21.1 KB

However, the system blew up and the error message was:
Error: segmentation violation

I would like to make a system consisting of 1 cation and 1 anion solvated by water using GROMACS after I figure out this issue.
Does anyone know how to figure it out?
Also, does anyone know how to make a system consisting of charged molecules?

Thanks a lot!

2

This seems to be more related to Gaussian than GROMACS. I’d think you’ll find better help elsewhere - at least I hope so.

3

There are many possibility could lead to this error, it needs more error message in ouput file to determine the reason. If you’re not familiar with Gaussian, you can divide this multitask file into separate task, which is more possible to find the error. By the way, I also have a doubt about the method and basis set in your .gjf file are not B3LYP/6-31+G**.
The process of making a system consisting charge is as same as a normal system containing small molecules, just need to set the right atom charge in the .top file.