How to solve LINCS error during NVT/NPT equilibration step

User discussions
1

GROMACS version: 2019.4
GROMACS modification: Yes

Dear Gromacs users,

Hello everyone. I’ve simulated Umbrella sampling for the DOPC bilayer and ligand system. My workflow is below:

  1. Generate ligand topology files by using ATB website(united atom representation)
  2. Concatenate the ligand and dopc structure file that is used to my simulation
  3. Energy minimization step with energy tolerance=500
  4. Run NVT equilibration

The EM is simulated with no problem, followed by NVT equilibration that caused the LINCS error. So I checked the em.gro-the output file of em step-with chimera and there was no problem. Below is the visualized em.gro wih chimera.

em
em1246×961 821 KB

(water is omitted and yellow is dopc molecules)

But when I opened the stepxxx.pdb file; result file of NVT LINCS error made by GROMCAS.

nvt
nvt1246×961 693 KB

(water is omitted and yellow is dopc molecules)

As you see, the nvt error file has broken bonds that means there is problem.

What occurs the problem?? When I proceeds the same workflow with another ligand, there was no problem.

Thank you

2

Have you run the ligand by itself to ensure the topology is stable?

3

I run the ligand nvt step by itself and it raised same errors.
The topology may be not stable

4

You’ll need to fix those first then.

5

How can I fix the topology file?

6

Non-trivial task, and need to know what you are doing. Go through the .itp file, checking the bonds and angles, ensuring they are consistent with the FF specifications and the atomtypes. The topology generating algorithm has probably gotten some of them wrong, they tend to stand out too.