# Too many LINCS warning; in MD run, NVT and NPT **URL:** https://gromacs.bioexcel.eu/t/too-many-lincs-warning-in-md-run-nvt-and-npt/5490 **Category:** User discussions **Created:** [December 27, 2022, 6:18am UTC](https://gromacs.bioexcel.eu/t/too-many-lincs-warning-in-md-run-nvt-and-npt/5490 "2022-12-27T06:18:29Z") **Posts on this page:** 1 **Page:** 1
### Author: ![arizthadp](https://avatars.discourse-cdn.com/v4/letter/a/35a633/32.png) [@arizthadp](https://gromacs.bioexcel.eu/u/arizthadp) #### Post date: [December 27, 2022, 6:18am UTC](https://gromacs.bioexcel.eu/t/too-many-lincs-warning-in-md-run-nvt-and-npt/5490/1 "2022-12-27T06:18:29Z")
GROMACS version: 2020.1 GROMACS modification: No Hello, i try running and protein-ligand complex simulation, but i got several errors when running MD simulations. I didn’t find this warning on the other ligand but on specific ligand, but my teammates also use same ligand and success. I find some solution in this forum and try to follow it but i can’t figure it out whats the problems on mine. Heres the error: Step 84098, time 168.196 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 161624336.000000, max 8174421504.000000 (between atoms 5161 and 5183) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 4537 4538 90.0 0.1128 0.1311 0.1111 4537 4539 76.5 0.2717 0.1233 0.1111 5161 5183 86.2 1937.3458 899186368.0000 0.1100 5163 5185 90.0 0.1111 0.2220 0.1111 step 84098: One or more water molecules can not be settled. Check for bad contacts and/or reduce the timestep if appropriate. Wrote pdb files with previous and current coordinates Segmentation fault (core dumped) theres several step that got LINCS warning, but i add one example here. theres another error when i try to runing again that said: "Warning: Only triclinic boxes with the first vector parallel to the x-axis and the second vector in the xy-plane are supported. " and its following with some boxes coordinate and heres my md.mdp file: title = Protein-ligand complex MD simulation ; Run parameters integrator = md ; leap-frog integrator nsteps = 5000000 ; 2 \* 5000000 = 10000 ps (10 ns) dt = 0.002 ; 2 fs ; Output control nstenergy = 5000 ; save energies every 10.0 ps nstlog = 5000 ; update log file every 10.0 ps nstxout-compressed = 5000 ; save coordinates every 10.0 ps ; Bond parameters continuation = yes ; continuing from NPT constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds to H are constrained lincs\_iter = 1 ; accuracy of LINCS lincs\_order = 4 ; also related to accuracy ; Neighbor searching and vdW cutoff-scheme = Verlet ns\_type = grid ; search neighboring grid cells nstlist = 20 ; largely irrelevant with Verlet rlist = 1.2 vdwtype = cutoff vdw-modifier = force-switch rvdw-switch = 1.0 rvdw = 1.2 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics rcoulomb = 1.2 pme\_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein\_LIG Water\_and\_ions ; 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 pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT pcoupltype = isotropic ; uniform scaling of box vectors tau\_p = 2.0 ; time constant, in ps ref\_p = 1.0 ; reference pressure, in bar compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1 ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction is not used for proteins with the C36 additive FF DispCorr = no ; Velocity generation gen\_vel = no ; continuing from NPT equilibration I already tried several times and still no changes. Thank you in advance!