I'm getting error as Floating point exception (core dumped) during energy minimization

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1

GROMACS version: 2024.1
GROMACS modification: No
Here post your question : I got this while running for energy minimization -
gmx mdrun -v -deffnm EM

Back Off! I just backed up EM.log to ./#EM.log.2#
Compiled SIMD is None, but AVX_512 might be faster (see log).
Reading file EM.tpr, VERSION 2024.1 (single precision)
1 GPU selected for this run.
Mapping of GPU IDs to the 1 GPU task in the 1 rank on this node:
PP:0
PP tasks will do (non-perturbed) short-ranged interactions on the GPU
PP task will update and constrain coordinates on the CPU
Using 1 MPI thread
Using 16 OpenMP threads

Back Off! I just backed up EM.trr to ./#EM.trr.2#

Back Off! I just backed up EM.edr to ./#EM.edr.2#

Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 50000
Step= 0, Dmax= 1.0e-02 nm, Epot= 6.00531e+04 Fmax= 3.58521e+05, atom= 4433
Step= 1, Dmax= 1.0e-02 nm, Epot= -3.22996e+04 Fmax= 3.44507e+05, atom= 4433
Step= 2, Dmax= 1.2e-02 nm, Epot= -9.95395e+04 Fmax= 3.30031e+05, atom= 4433
Step= 3, Dmax= 1.4e-02 nm, Epot= -1.54864e+05 Fmax= 3.15123e+05, atom= 4433
Step= 4, Dmax= 1.7e-02 nm, Epot= -2.03046e+05 Fmax= 3.00176e+05, atom= 4433
Step= 5, Dmax= 2.1e-02 nm, Epot= -2.46632e+05 Fmax= 2.85756e+05, atom= 4433
Step= 6, Dmax= 2.5e-02 nm, Epot= -2.87027e+05 Fmax= 2.71005e+05, atom= 4433
Step= 7, Dmax= 3.0e-02 nm, Epot= -3.24468e+05 Fmax= 2.52707e+05, atom= 4433
Step= 8, Dmax= 3.6e-02 nm, Epot= -3.59132e+05 Fmax= 2.28282e+05, atom= 4433
Step= 9, Dmax= 4.3e-02 nm, Epot= -3.93146e+05 Fmax= 1.93838e+05, atom= 4433
Step= 10, Dmax= 5.2e-02 nm, Epot= -4.27138e+05 Fmax= 1.97608e+05, atom= 4440
Step= 11, Dmax= 6.2e-02 nm, Epot= -4.51362e+05 Fmax= 1.26743e+05, atom= 4435
Step= 12, Dmax= 7.4e-02 nm, Epot= -4.88789e+05 Fmax= 6.38778e+04, atom= 4436
Step= 13, Dmax= 8.9e-02 nm, Epot= -5.35619e+05 Fmax= 6.13828e+04, atom= 4436
Step= 14, Dmax= 1.1e-01 nm, Epot= -5.65009e+05 Fmax= 5.94344e+04, atom= 4435
Step= 15, Dmax= 1.3e-01 nm, Epot= -5.86306e+05 Fmax= 5.09777e+04, atom= 4433
Step= 16, Dmax= 1.5e-01 nm, Epot= -5.94005e+05 Fmax= 3.12287e+05, atom= 4433
Floating point exception (core dumped)

Please anyone help me to solve.

Thank you.

2

I would recommend having a closer look at atoms 4433-4440. I suspect there are atoms overlapping (or being far too close to each other).

3

Can you please help me which File do I check to correct, Is it EM.tpr?

4

Check the .pdb or .gro file you used as input to gmx grompp.

5

This is the last input file before md run that I used as gmx grompp - “box_sol_ion.gro”. I had also added maxwarn 2 for the output EM.tpr, which had run successfully. I had checked the file "**box_sol_ion.gro ** but didn’t find any error.

6

In principle you should avoid using maxwarn, unless you are really sure about what you are doing.

When you say that you did not find any error in the .gro file, did you check how close the atoms (listed above) were to each other and other atoms?

7

This is the warning before I used Maxwarn 2 -

Command line:
gmx grompp -f EM.mdp -c box_sol_ion.gro -p topol.top -o EM.tpr

Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘ns_type’

NOTE 1 [file EM.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.

Setting the LD random seed to -271585035

Generated 22791 of the 22791 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1

Generated 19663 of the 22791 1-4 parameter combinations

Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’

Excluding 3 bonded neighbours molecule type ‘LIG’

Excluding 2 bonded neighbours molecule type ‘SOL’

Excluding 1 bonded neighbours molecule type ‘NA’

Excluding 1 bonded neighbours molecule type ‘CL’
Analysing residue names:
There are: 458 Protein residues
There are: 1 Other residues
There are: 15559 Water residues
There are: 75 Ion residues
Analysing Protein…
Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups…
Number of degrees of freedom in T-Coupling group rest is 115818.00
The integrator does not provide a ensemble temperature, there is no system ensemble temperature

The largest distance between excluded atoms is 1.441 nm between atom 4415 and 4436

WARNING 1 [file EM.mdp]:
The largest distance between excluded atoms is 1.441 nm between atom 4415
and 4436, which is larger than the cut-off distance. This will lead to
missing long-range corrections in the forces and energies. If you expect
that minimization will bring such distances within the cut-off, you can
ignore this warning.

Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 64x64x84, spacing 0.119 0.118 0.116

Estimate for the relative computational load of the PME mesh part: 0.06

This run will generate roughly 4 Mb of data

There was 1 NOTE

There was 1 WARNING

Program: gmx grompp, version 2024.1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2751)

Fatal error:
Too many warnings (1).
If you are sure all warnings are harmless, use the -maxwarn option.

Actually Sir, I’m newbie to Gromacs therefore, I find it little difficult to understand checking the gro file and trying to manipulate the file, kindly understand and please guide me to solve the issues. Thank you for your response.

8

Would you be able to upload the .gro file somewhere and post a link?

9

Thank you sir, here is the gdrive link for the .gro file - MD Simulations - Google Drive

10

There seems to be a problem with ASP 270. It is a terminal residue and seems uncapped. I don’t think pdb2gmx has recognized that there is a separation between two protein chains. I think you will have to go back to the original PDB structure and make sure that the termini are correct and then recreate the topology with pdb2gmx and pay extra attention to the termini so that they are properly identified.

11

Sir I have tried to modified by UCSF Chimera, but I couldn’t. Can you please guide me how I could correct, I have tried to capped by adding Hydrogen but I failed. It would be helpful if you could guide me Sir. Thank you.

12

I’m afraid I can’t give specific instructions, but I’d start by checking what the terminal residues are called in the force field you are using and rename them appropriately. Introducing TER lines in the PDB file (if there aren’t any) might also help gmx grompp understand where there are terminal residues. I’d recommend doing these edits of the PDB file using a text editor rather than Chimera.