Error in MD run for Energy Minimization step

User discussions
1

GROMACS version: 2020.3
GROMACS modification: Yes/No
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Respected all,
I am trying to do MDS for the protein-ligand complex. when I run the command: gmx mdrun -v -deffnm em and I am getting error
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Floating point exception (core dumped)
Please help me to clear the error.
Thanks in advance

Regards,
Jyothi

2

http://manual.gromacs.org/current/user-guide/terminology.html#diagnosing-an-unstable-system

3

Thank you so much Mr. Jalemkul it is very helpful to understand the problem.

4

Greetings!!!
I have gone through the manual and checked my process. Everything was fine. I was able to run MD simulations for my protein alone but when I am running with docked complex, getting note like core dumped. I tried with another ligand and getting the same not for that protein. IF problem is in gromacs installation then how could it possible to run MD for other proteins?
I will be highly grateful if I get the reason. I had tried but didn’t get any proper reason for that note ‘Floating point exception (core dumped)’

5

See the link I posted above about diagnosing an unstable system. If adding the ligand causes an immediate crash, then maybe your topology is unusable and requires further scrutiny.

6

Thank you for your response. I will check it out.

Regards,
Jyothi