How to fix the LINCS warning problems during MD running that orignially obtained from Chamm-gui

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1

GROMACS version: 2022.1
GROMACS modification: No

Dear Sir,
I am a new one.
I would like to ask a question. During running MD simulation, I got warning information.
For example, I got the warning information: " Step 2496567, time 9986.27 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000196, max 0.003065 (between atoms 4041 and 4044) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4041 4043 31.5 0.1091 0.1088 0.1090 step 2496600, remaining wall clock time: 10 s

". Anyone could help me know how can I fix the LINCS WARNING？

Note, I prepared my MD simulation (ligand-protein complex) that got from CHARMM-GUI (Amber force field: ff19sb, OPC water model, gaff2, hydrogen mass repartitioning (HMR))

my md_production.mdp:

integrator = md
dt = 0.004
nsteps = 2500000
nstxtcout = 25000
nstvout = 25000
nstfout = 25000
nstcalcenergy = 100
nstenergy = 1000
nstlog = 1000
;
cutoff-scheme = Verlet
nstlist = 20
vdwtype = Cut-off
vdw-modifier = None
DispCorr = EnerPres
rvdw = 0.9
rlist = 0.9
rcoulomb = 0.9
coulombtype = PME
;
tcoupl = V-rescale
tc_grps = SOLU SOLV
tau_t = 1.0 1.0
ref_t = 310 310
;
pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 5.0
compressibility = 4.5e-5
ref_p = 1.0
;
constraints = h-bonds
constraint_algorithm = LINCS
continuation = yes
;
nstcomm = 100
comm_mode = linear
comm_grps = SOLU SOLV

Thank you very much

2

Hi. I’m having this issue as well (charmm forcefield) but only when I run the simulation over multiple nodes. I’m wondering if there is a bug or we need to use LINCS more carefully.

It helps if you can use constraints = all-bonds