EM converge before reaching the target steps, NVT indicated segmentation fault

User discussions
1

GROMACS version: 2023.1
GROMACS modification: NO

Good day

I am simulating 200 molecules of tetrabutylphosphonium phosphate ionic liquids in a cubic box.

Unfortunately, EM step converged before reaching targeted Fmax on the atoms and the proceeding NVT step do crashed by indicating segmentation fault.

I will appreciate your help and support. The .tpr and .mdp files are attached.

em.mdp (952 Bytes)
nvt.mdp (2.0 KB)

tbpppt_em.tpr

2

I don’t think it’s a problem with your MDP parameters, but that the input structure may be unfavourable. Check the console output when you run the energy minimization. Look for the atoms with highest force and examine their surroundings in a visualisation program.

Otherwise you could run an additional NVT equilibration before your current one. Use the same settings as in nvt.mdp, except

dt = 0.0005

You might also want to lower the temperature in the first NVT step to slow things down. Run a second NVT equilibration with your current settings. That might give your system a chance to fix itself, unless there are atoms colliding.

3

Thank you @MagnusL for your help.

This is the information after EM step

Step=   79, Dmax= 2.0e-06 nm, Epot= -1.92779e+05 Fmax= 1.07810e+05, atom= 11142
Step=   81, Dmax= 1.2e-06 nm, Epot= -1.92779e+05 Fmax= 1.01848e+05, atom= 11146
Energy minimization has stopped, but the forces have not converged to the
requested precision Fmax < 100 (which may not be possible for your system).
It stopped because the algorithm tried to make a new step whose size was too
small, or there was no change in the energy since last step. Either way, we
regard the minimization as converged to within the available machine
precision, given your starting configuration and EM parameters.

Double precision normally gives you higher accuracy, but this is often not
needed for preparing to run molecular dynamics.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 82 steps,
but did not reach the requested Fmax < 100.
Potential Energy  = -1.9277866e+05
Maximum force     =  1.0781029e+05 on atom 11142
Norm of force     =  1.3809802e+03

GROMACS reminds you: "Problems worthy of attack prove their worth by hitting back." (Piet Hein)

Now:

  1. I have no idea on which atom to visualize and correct.
  2. I run the NVT at low temperature as you suggested, with dt = 0.0005 but still got the same problem.
4

Have a look at atoms 11142 and 11146, and preferably atoms close to them. E.g., within 2 of index 11141 11145 should work in VMD, I think.

5

I can open the structure file in a text editor or VMD. When I opened it in VMD, I can switch from one drawing method to another, change the background color, and show the simulation box but I have no idea of selecting and manipulating a specific atom in the system within VMD. I try to figure it out but to no avail. Any hep on that please?

6

That is more of a VMD question. But anyhow, start having a look at Graphical Representations in the Graphics menu. In there you can use the Selected Atoms box to show what you want, e.g., within 2 of index 11141 11145.