Lincs warning during Npt equillibriation step

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
Here post your question
Hi, I am running a CG simulation of a large system during minimization I received 6 linics warning and the system ran and converged. After that, I moved to equilibration and grompp ran and during md run I got 1116 linics warnings. I have tried rdd-1.4 and also increased the radius of water nothing works still the error comes. I try to remove the water beads it reduces the density.Some help me with this. Looking forward to hearing from you.
mail:vv213628@gmail.com
Thank you in advance

2

This indicates an instability of the system. Modifying, e.g., the radius of water is almost certainly not the way to resolve it.

You say the crash (you didn’t explicitly say it crashed, but I assume it did) occurs during NPT equilibration. Did the NVT equilibration stage pass? In general, if you get crashes like this you can usually resolve them by running one or two extra NVT equilibration simulations, the first one with very small integration time step and possibly with increased restraints. That can then be followed by another NVT stage with slightly larger timesteps and possibly the same restraints as you would use during NVT. An example protocol would be:

  • EM
  • NVT, dt = 0.0002, nsteps = 50000 (higher restraints if needed)
  • NVT, dt = 0.001, nsteps = 100000
  • NVT, dt = 0.002, nsteps = 500000 (or whatever is suitable for your system)
  • NPT
  • Production simulations

If it still fails, you could try reducing the temperature in the first two NVT equilibration stages.