Too many Lincs warning

User discussions
1

GROMACS version: 2018.1
GROMACS modification: No
I am trying to simulate water and tertiary butanol binary mixture. But in the energy minimization step I found Fatal error: Too many lincs warning (1233) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem.
My em.mdp file is given below:
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 100.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Minimization step size
nsteps = 10000 ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions in all 3 dimensions
constraints = allbonds
constraint_algorithm = lincs

I am learning md simulation using Gromacs for last couple of months. It will be very helpful if you could give some input in this regard.
thank you

2

Quick questions:

What happens if you run just a single butanol molecule? I am wondering if the initial coordinates for your butanol model are the source of your troubles.

Also: why are you restraining all-bonds?

3

Thank you Mick for your kind concern. Lincs warning is still coming when i run with only teriary butanol molecule. Without restraining the all bonds potential energy has become highly positive after energy minimization. Awaiting for your valuable input.

4

Your observation suggests an unstable topology. How did you parametrize the molecule?

5

Thank you jalemkul. All the force field parameter value i have taken from a paper and using those value i have created topology file.