LINCS Error in production run

User discussions
, ,
1

GROMACS version: 2021.1
GROMACS modification: Yes/No
Here post your question

I am currently running a 1 ns production molecular dynamics (MD) simulation with restraints, but I’m encountering persistent LINCS warnings that are causing the simulation to terminate. Despite extensive troubleshooting (15-20 alterations in the mdp file), including additional equilibration and restarting the simulation from scratch, the issue remains unresolved.
Any suggestions on what else I can try.

2

Without more information, it is difficult to come with any reasonable suggestions. I presume that the energy minimization finished OK, right? You say that you have tried additional equilibration, was that in both NVT and NPT ensembles? What was the difference between the equilibration (that presumably did not crash) and the simulation that did crash?

A few things that often cause these crashes:

  • Are there any atoms overlapping or bonds that are unrealistically long? This is usually addressed by energy minimization, so possibly not relevant here.
  • Is the structure that you are using as reference for restraints similar enough to the structure the simulation (that crashes) is starting from?
  • If you are using a barostat, is it suitable (c-rescale) and/or is the pressure coupling constant (tau-p) suitable (2 to 10 ps, but this is more important if you are using, e.g., parrinello-rahman for pressure coupling)?
  • Are your force field parameters correct?