# System blowing up with lincs warning after considerable number of steps **URL:** \ **Category:** User discussions\ **Created:** [December 22, 2024, 3:26pm UTC](https://gromacs.bioexcel.eu/t/system-blowing-up-with-lincs-warning-after-considerable-number-of-steps/10883 "2024-12-22T15:26:57Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![AnanyaC](https://avatars.discourse-cdn.com/v4/letter/a/8797f3/32.png) [@AnanyaC](https://gromacs.bioexcel.eu/u/AnanyaC)\ **Post date:** [December 22, 2024, 3:26pm UTC](https://gromacs.bioexcel.eu/t/system-blowing-up-with-lincs-warning-after-considerable-number-of-steps/10883/1 "2024-12-22T15:26:57Z")
GROMACS version: GROMACS modification: Yes/No Hi, I am running a simulation of protein DNA complex with some modification in the proteins. I used parameterized the residues with ambertools, and incorporated them accordingly with gromacs manual. Did gradual EM till emtol=100, equilibrated considerably and went for production run. After running for some considerable steps the lincs warning appears. Any suggestions will be helpful . The warning is as given below, Step 141822, time 141.822 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000004, max 0.000016 (between atoms 20108 and 20110) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 99 100 78.0 0.0960 0.0960 0.0960 Step 141823, time 141.823 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000004, max 0.000016 (between atoms 20818 and 20820) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 99 100 77.6 0.0960 0.0960 0.0960 Step 141824, time 141.824 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.000004, max 0.000017 (between atoms 16038 and 16039) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 99 100 77.2 0.0960 0.0960 0.0960 * * * Program: gmx mdrun, version 2022.3 Source file: src/gromacs/mdlib/constr.cpp (line 240) Fatal error: Too many LINCS warnings (1000) 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 , the mdp parameters that i am using are: title = OPLS Lysozyme NPT equilibration ; Run parameters integrator = md ; leap-frog integrator nsteps = 10000000 ; 100 ns dt = 0.001 ; 2 fs ; Output control nstxout = 0 ; suppress bulky .trr file by specifying nstvout = 0 ; 0 for output frequency of nstxout, nstfout = 0 ; nstvout, and nstfout nstenergy = 50000 ; save energies every 100.0 ps nstlog = 50000 ; update log file every 100.0 ps nstxout-compressed = 50000 ; save compressed coordinates every 100.0 ps compressed-x-grps = System ; save the whole system ; Bond parameters continuation = yes ; Restarting after NPT constraint\_algorithm = lincs ; holonomic constraints constraints = h-bonds ; bonds involving H are constrained lincs\_iter =1 ; lincs\_order =6 ; ; Neighborsearching cutoff-scheme = Verlet ; Buffered neighbor searching ns\_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme rcoulomb = 2.1 ; short-range electrostatic cutoff (in nm) rvdw = 2.1 ; short-range van der Waals cutoff (in nm) epsilon\_rf =78.0 ; ; Electrostatics coulombtype = reaction-field ; 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 on pcoupl = C-rescale ; Pressure coupling on in 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 DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen\_vel = no ; Velocity generation is off ---
**Author:** ![askforarun](https://avatars.discourse-cdn.com/v4/letter/a/c5a1d2/32.png) [@askforarun](https://gromacs.bioexcel.eu/u/askforarun)\ **Post date:** [December 23, 2024, 12:21am UTC](https://gromacs.bioexcel.eu/t/system-blowing-up-with-lincs-warning-after-considerable-number-of-steps/10883/2 "2024-12-23T00:21:19Z")
This could be a problem with system setup. Do you get the same warnings when you use 1 fs timstep ? ---
**Author:** ![AnanyaC](https://avatars.discourse-cdn.com/v4/letter/a/8797f3/32.png) [@AnanyaC](https://gromacs.bioexcel.eu/u/AnanyaC)\ **Post date:** [December 25, 2024, 12:29pm UTC](https://gromacs.bioexcel.eu/t/system-blowing-up-with-lincs-warning-after-considerable-number-of-steps/10883/3 "2024-12-25T12:29:28Z")
yes. the error persists. Also, the bond parameters, such as angles and dihedrals how are they to be confirmed whether i am using them right? ---
**Author:** ![askforarun](https://avatars.discourse-cdn.com/v4/letter/a/c5a1d2/32.png) [@askforarun](https://gromacs.bioexcel.eu/u/askforarun)\ **Post date:** [December 25, 2024, 4:29pm UTC](https://gromacs.bioexcel.eu/t/system-blowing-up-with-lincs-warning-after-considerable-number-of-steps/10883/4 "2024-12-25T16:29:10Z")
Its hard to diagnose with the information you have given. What is the force field you are using ? How are the force field parameters generated? ---
**Author:** ![AnanyaC](https://avatars.discourse-cdn.com/v4/letter/a/8797f3/32.png) [@AnanyaC](https://gromacs.bioexcel.eu/u/AnanyaC)\ **Post date:** [December 25, 2024, 6:22pm UTC](https://gromacs.bioexcel.eu/t/system-blowing-up-with-lincs-warning-after-considerable-number-of-steps/10883/5 "2024-12-25T18:22:51Z")
I am using amber99sb.ff. the forcefield parameters for the modified residue is generated using antechamber-acpype. But the bond-type, angles and dihedral types for joining the modified residue and main chain are not obtained by acpype.