GROMACS version: 2019
Hi Gromacs users,
I am simulating a Ligand-Protein complex and I am getting the following LINCS errors while running the NVT equilibration;
Step 129, time 0.258 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000005, max 0.000027 (between atoms 25756 and 25758)
bonds that rotated more than 30 degrees:
- atom 1 atom 2 angle previous, current, constraint length*
- 8077 8078 46.6 0.1000 0.1000 0.1000*
Step 130, time 0.26 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000005, max 0.000018 (between atoms 23872 and 23873)
bonds that rotated more than 30 degrees:
- atom 1 atom 2 angle previous, current, constraint length*
- 8077 8078 37.9 0.1000 0.1000 0.1000*
Step 131, time 0.262 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000005, max 0.000027 (between atoms 8213 and 8214)
bonds that rotated more than 30 degrees:
- atom 1 atom 2 angle previous, current, constraint length*
- 8077 8078 31.2 0.1000 0.1000 0.1000*
Fatal error:
Too many LINCS warnings (1002)
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.
Please note that the errors are in the N-H bonds;
8077 (N) 8078 (H)
25756 (NZ) and 25758 (HH11)
23872 (NT) and 23873 (HD21)
ARG: 8213 (NZ) and 8214 (HH11)
The energy minimization converges :
Steepest Descents converged to Fmax < 1000 in 2559 steps
Potential Energy = -6.7342790e+06
Maximum force = 9.9927802e+02 on atom 8041
Norm of force = 1.0815428e+01
My mdp file is:
title = NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 500 ; save coordinates every 1.0 ps
nstvout = 500 ; save velocities every 1.0 ps
nstenergy = 500 ; save energies every 1.0 ps
nstlog = 500 ; update log file every 1.0 ps
; Bond parameters
continuation = no ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = h-bonds ; bonds involving H are constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Nonbonded settings
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rlist = 1.4 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
DispCorr = EnerPres ; account for cut-off vdW scheme
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling is off
pcoupl = no ; no pressure coupling in NVT
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Velocity generation
gen_vel = yes ; assign velocities from Maxwell distribution
gen_temp = 300 ; temperature for Maxwell distribution
gen_seed = -1 ; generate a random seed
I would appreciate any help.
Deniz