# LINCS warnings
**URL:** https://gromacs.bioexcel.eu/t/lincs-warnings/775
**Category:** User discussions
**Created:** [September 6, 2020, 3:59am UTC](https://gromacs.bioexcel.eu/t/lincs-warnings/775 "2020-09-06T03:59:03Z")
**Posts on this page:** 7
**Page:** 1
### Author:  [@kw24](https://gromacs.bioexcel.eu/u/kw24)
#### Post date: [September 6, 2020, 3:59am UTC](https://gromacs.bioexcel.eu/t/lincs-warnings/775/1 "2020-09-06T03:59:04Z")
GROMACS version: 2020.3
GROMACS modification: No
I’ve been trying to heat up 4 polystyrene chains from 300K up to 1200K with a series of NVT simulations that have “continuation=yes” and a .cpt file from the previous NVT grompped in, but I always encounter an error with LINCS. Over my several attempts, the error shows up usually after my NVT at 600K. I tried to work through it by not including a .cpt file from the previous NVT, setting continuation=no, and “gen\_v=yes” to run each NVT separately as I heat up my system. Suffice it to say, I keep experiencing a LINCS error. Can anyone help?
Here’s one of my log files:
> ```
> > GROMACS: gmx mdrun, version 2020.3
> > Executable: /usr/local/gromacs/bin/gmx
> > Data prefix: /usr/local/gromacs
> > Working dir: /Users/profile1/Desktop/gromacs-related_work/NPs_BBB/PS/PSNP/PSNP4
> > Process ID: 13756
> > Command line:
> > gmx mdrun -deffnm nvt1100 -v -nt 1 -pin on
> >
> > GROMACS version: 2020.3
> > Verified release checksum is c0599e547549c2d0ef4fc678dc5a26ad0000eab045e938fed756f9ff5b99a197
> > Precision: single
> > Memory model: 64 bit
> > MPI library: thread_mpi
> > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
> > GPU support: OpenCL
> > SIMD instructions: AVX2_256
> > FFT library: fftw-3.3.8-sse2
> > RDTSCP usage: enabled
> > TNG support: enabled
> > Hwloc support: disabled
> > Tracing support: disabled
> > C compiler: /usr/local/bin/icc Intel 19.1.2.20200623
> > C compiler flags: -march=core-avx2 -std=gnu99 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -O3 -DNDEBUG
> > C++ compiler: /usr/local/bin/icpc Intel 19.1.2.20200623
> > C++ compiler flags: -march=core-avx2 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -qopenmp -O3 -DNDEBUG
> > OpenCL include dir: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/OpenCL.framework
> > OpenCL library: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/OpenCL.framework
> > OpenCL version: 1.2
> >
> >
> > Running on 1 node with total 4 cores, 4 logical cores, 0 compatible GPUs
> > Hardware detected:
> > CPU info:
> > Vendor: Intel
> > Brand: Intel(R) Core(TM) i5-4570R CPU @ 2.70GHz
> > Family: 6 Model: 70 Stepping: 1
> > Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> > Hardware topology: Only logical processor count
> > GPU info:
> > Number of GPUs detected: 1
> > #0: name: Iris Pro, vendor: Intel, device version: OpenCL 1.2 , stat: incompatible (please recompile with GMX_OPENCL_NB_CLUSTER_SIZE=4)
> >
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
> > Lindahl
> > GROMACS: High performance molecular simulations through multi-level
> > parallelism from laptops to supercomputers
> > SoftwareX 1 (2015) pp. 19-25
> > -------- -------- --- Thank You --- -------- --------
> >
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
> > Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
> > GROMACS
> > In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
> > -------- -------- --- Thank You --- -------- --------
> >
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
> > Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
> > GROMACS 4.5: a high-throughput and highly parallel open source molecular
> > simulation toolkit
> > Bioinformatics 29 (2013) pp. 845-54
> > -------- -------- --- Thank You --- -------- --------
> >
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
> > GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
> > molecular simulation
> > J. Chem. Theory Comput. 4 (2008) pp. 435-447
> > -------- -------- --- Thank You --- -------- --------
> >
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
> > Berendsen
> > GROMACS: Fast, Flexible and Free
> > J. Comp. Chem. 26 (2005) pp. 1701-1719
> > -------- -------- --- Thank You --- -------- --------
> >
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > E. Lindahl and B. Hess and D. van der Spoel
> > GROMACS 3.0: A package for molecular simulation and trajectory analysis
> > J. Mol. Mod. 7 (2001) pp. 306-317
> > -------- -------- --- Thank You --- -------- --------
> >
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > H. J. C. Berendsen, D. van der Spoel and R. van Drunen
> > GROMACS: A message-passing parallel molecular dynamics implementation
> > Comp. Phys. Comm. 91 (1995) pp. 43-56
> > -------- -------- --- Thank You --- -------- --------
> >
> >
> > ++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
> > https://doi.org/10.5281/zenodo.3923645
> > -------- -------- --- Thank You --- -------- --------
> >
> > Input Parameters:
> > integrator = md
> > tinit = 0
> > dt = 0.025
> > nsteps = 80000
> > init-step = 0
> > simulation-part = 1
> > comm-mode = Linear
> > nstcomm = 100
> > bd-fric = 0
> > ld-seed = -201697359
> > emtol = 10
> > emstep = 0.01
> > niter = 20
> > fcstep = 0
> > nstcgsteep = 1000
> > nbfgscorr = 10
> > rtpi = 0.05
> > nstxout = 0
> > nstvout = 0
> > nstfout = 0
> > nstlog = 1000
> > nstcalcenergy = 100
> > nstenergy = 100
> > nstxout-compressed = 1000
> > compressed-x-precision = 100
> > cutoff-scheme = Verlet
> > nstlist = 15
> > pbc = xyz
> > periodic-molecules = false
> > verlet-buffer-tolerance = 0.005
> > rlist = 1.14
> > coulombtype = Reaction-Field
> > coulomb-modifier = Potential-shift
> > rcoulomb-switch = 0
> > rcoulomb = 1.1
> > epsilon-r = 15
> > epsilon-rf = inf
> > vdw-type = Cut-off
> > vdw-modifier = Potential-shift
> > rvdw-switch = 0
> > rvdw = 1.1
> > DispCorr = No
> > table-extension = 1
> > fourierspacing = 0.12
> > fourier-nx = 0
> > fourier-ny = 0
> > fourier-nz = 0
> > pme-order = 4
> > ewald-rtol = 1e-05
> > ewald-rtol-lj = 0.001
> > lj-pme-comb-rule = Geometric
> > ewald-geometry = 0
> > epsilon-surface = 0
> > tcoupl = Nose-Hoover
> > nsttcouple = 15
> > nh-chain-length = 1
> > print-nose-hoover-chain-variables = false
> > pcoupl = No
> > pcoupltype = Isotropic
> > nstpcouple = -1
> > tau-p = 1
> > compressibility (3x3):
> > compressibility[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > compressibility[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > compressibility[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > ref-p (3x3):
> > ref-p[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > ref-p[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > ref-p[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > refcoord-scaling = No
> > posres-com (3):
> > posres-com[0]= 0.00000e+00
> > posres-com[1]= 0.00000e+00
> > posres-com[2]= 0.00000e+00
> > posres-comB (3):
> > posres-comB[0]= 0.00000e+00
> > posres-comB[1]= 0.00000e+00
> > posres-comB[2]= 0.00000e+00
> > QMMM = false
> > QMconstraints = 0
> > QMMMscheme = 0
> > MMChargeScaleFactor = 1
> > qm-opts:
> > ngQM = 0
> > constraint-algorithm = Lincs
> > continuation = false
> > Shake-SOR = false
> > shake-tol = 0.0001
> > lincs-order = 4
> > lincs-iter = 1
> > lincs-warnangle = 30
> > nwall = 0
> > wall-type = 9-3
> > wall-r-linpot = -1
> > wall-atomtype[0] = -1
> > wall-atomtype[1] = -1
> > wall-density[0] = 0
> > wall-density[1] = 0
> > wall-ewald-zfac = 3
> > pull = false
> > awh = false
> > rotation = false
> > interactiveMD = false
> > disre = No
> > disre-weighting = Conservative
> > disre-mixed = false
> > dr-fc = 1000
> > dr-tau = 0
> > nstdisreout = 100
> > orire-fc = 0
> > orire-tau = 0
> > nstorireout = 100
> > free-energy = no
> > cos-acceleration = 0
> > deform (3x3):
> > deform[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > deform[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > deform[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > simulated-tempering = false
> > swapcoords = no
> > userint1 = 0
> > userint2 = 0
> > userint3 = 0
> > userint4 = 0
> > userreal1 = 0
> > userreal2 = 0
> > userreal3 = 0
> > userreal4 = 0
> > applied-forces:
> > electric-field:
> > x:
> > E0 = 0
> > omega = 0
> > t0 = 0
> > sigma = 0
> > y:
> > E0 = 0
> > omega = 0
> > t0 = 0
> > sigma = 0
> > z:
> > E0 = 0
> > omega = 0
> > t0 = 0
> > sigma = 0
> > density-guided-simulation:
> > active = false
> > group = protein
> > similarity-measure = inner-product
> > atom-spreading-weight = unity
> > force-constant = 1e+09
> > gaussian-transform-spreading-width = 0.2
> > gaussian-transform-spreading-range-in-multiples-of-width = 4
> > reference-density-filename = reference.mrc
> > nst = 1
> > normalize-densities = true
> > adaptive-force-scaling = false
> > adaptive-force-scaling-time-constant = 4
> > grpopts:
> > nrdf: 3597
> > ref-t: 1100
> > tau-t: 7.5
> > annealing: No
> > annealing-npoints: 0
> > acc: 0 0 0
> > nfreeze: N N N
> > energygrp-flags[0]: 0
> >
> > Changing nstlist from 15 to 25, rlist from 1.14 to 1.288
> >
> > Using 1 MPI thread
> > Using 1 OpenMP thread
> >
> > System total charge: 0.000
> > Reaction-Field:
> > epsRF = 0, rc = 1.1, krf = 0.375657, crf = 1.36364, epsfac = 9.26236
> > The electrostatics potential has its minimum at r = 1.1
> > Potential shift: LJ r^-12: -3.186e-01 r^-6: -5.645e-01
> >
> > Using SIMD 4x8 nonbonded short-range kernels
> >
> > Using a dual 4x8 pair-list setup updated with dynamic pruning:
> > outer list: updated every 25 steps, buffer 0.188 nm, rlist 1.288 nm
> > inner list: updated every 12 steps, buffer 0.004 nm, rlist 1.104 nm
> > At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
> > outer list: updated every 25 steps, buffer 0.309 nm, rlist 1.409 nm
> > inner list: updated every 12 steps, buffer 0.038 nm, rlist 1.138 nm
> >
> > Using full Lennard-Jones parameter combination matrix
> >
> > Removing pbc first time
> >
> > Initializing LINear Constraint Solver
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > B. Hess
> > P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
> > J. Chem. Theory Comput. 4 (2008) pp. 116-122
> > -------- -------- --- Thank You --- -------- --------
> >
> > The number of constraints is 1200
> > 1200 constraints are involved in constraint triangles,
> > will apply an additional matrix expansion of order 4 for couplings
> > between constraints inside triangles
> > There are: 1600 Atoms
> >
> > Constraining the starting coordinates (step 0)
> >
> > Constraining the coordinates at t0-dt (step 0)
> > Center of mass motion removal mode is Linear
> > We have the following groups for center of mass motion removal:
> > 0: rest
> > RMS relative constraint deviation after constraining: 7.39e-05
> > Initial temperature: 1107.37 K
> >
> > Started mdrun on rank 0 Sat Sep 5 22:22:27 2020
> >
> > Step Time
> > 0 0.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.28960e+03 8.66453e+03 -1.53340e+04 0.00000e+00 -3.37990e+03
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.75872e+04 1.42073e+04 1.42073e+04 1.17612e+03 4.25599e+00
> > Constr. rmsd
> > 8.12963e-05
> >
> > Step Time
> > 1000 25.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.66045e+03 8.90748e+03 -1.38989e+04 0.00000e+00 -1.33095e+03
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.59711e+04 1.46402e+04 1.57249e+04 1.06805e+03 -8.33768e-01
> > Constr. rmsd
> > 6.50159e-05
> >
> > Step Time
> > 2000 50.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.82262e+03 9.45960e+03 -1.41411e+04 0.00000e+00 -8.58900e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.64603e+04 1.56014e+04 1.65575e+04 1.10076e+03 -2.60957e-01
> > Constr. rmsd
> > 7.25666e-05
> >
> > Step Time
> > 3000 75.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.56032e+03 9.10781e+03 -1.34891e+04 0.00000e+00 -8.20996e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.58069e+04 1.49860e+04 1.79927e+04 1.05707e+03 2.79133e-01
> > Constr. rmsd
> > 6.68478e-05
> >
> > Step Time
> > 4000 100.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.74427e+03 9.34828e+03 -1.36906e+04 0.00000e+00 -5.98027e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.67469e+04 1.61489e+04 1.94894e+04 1.11993e+03 2.93788e+00
> > Constr. rmsd
> > 7.30774e-05
> >
> > Step Time
> > 5000 125.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.81480e+03 9.13224e+03 -1.37587e+04 0.00000e+00 -8.11626e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.67623e+04 1.59507e+04 2.07879e+04 1.12096e+03 -2.00317e+00
> > Constr. rmsd
> > 6.81476e-05
> >
> > Step Time
> > 6000 150.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.46302e+03 9.35158e+03 -1.44799e+04 0.00000e+00 -1.66528e+03
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.75189e+04 1.58536e+04 2.24366e+04 1.17155e+03 1.42028e+00
> > Constr. rmsd
> > 8.72229e-05
> >
> > Step Time
> > 7000 175.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.75645e+03 9.79785e+03 -1.38365e+04 0.00000e+00 -2.82240e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.84950e+04 1.82128e+04 2.35599e+04 1.23683e+03 -6.79238e-01
> > Constr. rmsd
> > 9.62320e-05
> >
> > Constraint error in algorithm Lincs at step 7550
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 7551
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 7552
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 7553
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 7554
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 7555
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 7556
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 7557
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 7558
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 7559
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 7560
> > Wrote pdb files with previous and current coordinates
> >
> > -------------------------------------------------------
> > Program: gmx mdrun, version 2020.3
> > Source file: src/gromacs/mdlib/constr.cpp (line 224)
> >
> > 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
> >
> > For more information and tips for troubleshooting, please check the GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
>
> ```
Thank you!
---
### Author:  [@kw24](https://gromacs.bioexcel.eu/u/kw24)
#### Post date: [September 6, 2020, 4:01am UTC](https://gromacs.bioexcel.eu/t/lincs-warnings/775/2 "2020-09-06T04:01:54Z")
Here’s another .log file with a slightly different error:
> ```
> > GROMACS: gmx mdrun, version 2020.3
> > Executable: /usr/local/gromacs/bin/gmx
> > Data prefix: /usr/local/gromacs
> > Working dir: /Users/profile1/Desktop/gromacs-related_work/NPs_BBB/PS/PSNP/PSNP5
> > Process ID: 13767
> > Command line:
> > gmx mdrun -deffnm nvt1100 -v -nt 1
> >
> > GROMACS version: 2020.3
> > Verified release checksum is c0599e547549c2d0ef4fc678dc5a26ad0000eab045e938fed756f9ff5b99a197
> > Precision: single
> > Memory model: 64 bit
> > MPI library: thread_mpi
> > OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64)
> > GPU support: OpenCL
> > SIMD instructions: AVX2_256
> > FFT library: fftw-3.3.8-sse2
> > RDTSCP usage: enabled
> > TNG support: enabled
> > Hwloc support: disabled
> > Tracing support: disabled
> > C compiler: /usr/local/bin/icc Intel 19.1.2.20200623
> > C compiler flags: -march=core-avx2 -std=gnu99 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -O3 -DNDEBUG
> > C++ compiler: /usr/local/bin/icpc Intel 19.1.2.20200623
> > C++ compiler flags: -march=core-avx2 -ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14 -qoverride-limits -qopenmp -O3 -DNDEBUG
> > OpenCL include dir: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/OpenCL.framework
> > OpenCL library: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/System/Library/Frameworks/OpenCL.framework
> > OpenCL version: 1.2
> >
> >
> > Running on 1 node with total 4 cores, 4 logical cores, 0 compatible GPUs
> > Hardware detected:
> > CPU info:
> > Vendor: Intel
> > Brand: Intel(R) Core(TM) i5-4570R CPU @ 2.70GHz
> > Family: 6 Model: 70 Stepping: 1
> > Features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> > Hardware topology: Only logical processor count
> > GPU info:
> > Number of GPUs detected: 1
> > #0: name: Iris Pro, vendor: Intel, device version: OpenCL 1.2 , stat: incompatible (please recompile with GMX_OPENCL_NB_CLUSTER_SIZE=4)
> >
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > M. J. Abraham, T. Murtola, R. Schulz, S. Páll, J. C. Smith, B. Hess, E.
> > Lindahl
> > GROMACS: High performance molecular simulations through multi-level
> > parallelism from laptops to supercomputers
> > SoftwareX 1 (2015) pp. 19-25
> > -------- -------- --- Thank You --- -------- --------
> >
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > S. Páll, M. J. Abraham, C. Kutzner, B. Hess, E. Lindahl
> > Tackling Exascale Software Challenges in Molecular Dynamics Simulations with
> > GROMACS
> > In S. Markidis & E. Laure (Eds.), Solving Software Challenges for Exascale 8759 (2015) pp. 3-27
> > -------- -------- --- Thank You --- -------- --------
> >
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R.
> > Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl
> > GROMACS 4.5: a high-throughput and highly parallel open source molecular
> > simulation toolkit
> > Bioinformatics 29 (2013) pp. 845-54
> > -------- -------- --- Thank You --- -------- --------
> >
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > B. Hess and C. Kutzner and D. van der Spoel and E. Lindahl
> > GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable
> > molecular simulation
> > J. Chem. Theory Comput. 4 (2008) pp. 435-447
> > -------- -------- --- Thank You --- -------- --------
> >
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A. E. Mark and H. J. C.
> > Berendsen
> > GROMACS: Fast, Flexible and Free
> > J. Comp. Chem. 26 (2005) pp. 1701-1719
> > -------- -------- --- Thank You --- -------- --------
> >
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > E. Lindahl and B. Hess and D. van der Spoel
> > GROMACS 3.0: A package for molecular simulation and trajectory analysis
> > J. Mol. Mod. 7 (2001) pp. 306-317
> > -------- -------- --- Thank You --- -------- --------
> >
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > H. J. C. Berendsen, D. van der Spoel and R. van Drunen
> > GROMACS: A message-passing parallel molecular dynamics implementation
> > Comp. Phys. Comm. 91 (1995) pp. 43-56
> > -------- -------- --- Thank You --- -------- --------
> >
> >
> > ++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++
> > https://doi.org/10.5281/zenodo.3923645
> > -------- -------- --- Thank You --- -------- --------
> >
> > Input Parameters:
> > integrator = md
> > tinit = 0
> > dt = 0.025
> > nsteps = 80000
> > init-step = 0
> > simulation-part = 1
> > comm-mode = Linear
> > nstcomm = 100
> > bd-fric = 0
> > ld-seed = 410085841
> > emtol = 10
> > emstep = 0.01
> > niter = 20
> > fcstep = 0
> > nstcgsteep = 1000
> > nbfgscorr = 10
> > rtpi = 0.05
> > nstxout = 0
> > nstvout = 0
> > nstfout = 0
> > nstlog = 1000
> > nstcalcenergy = 100
> > nstenergy = 100
> > nstxout-compressed = 1000
> > compressed-x-precision = 100
> > cutoff-scheme = Verlet
> > nstlist = 15
> > pbc = xyz
> > periodic-molecules = false
> > verlet-buffer-tolerance = 0.005
> > rlist = 1.14
> > coulombtype = Reaction-Field
> > coulomb-modifier = Potential-shift
> > rcoulomb-switch = 0
> > rcoulomb = 1.1
> > epsilon-r = 15
> > epsilon-rf = inf
> > vdw-type = Cut-off
> > vdw-modifier = Potential-shift
> > rvdw-switch = 0
> > rvdw = 1.1
> > DispCorr = No
> > table-extension = 1
> > fourierspacing = 0.12
> > fourier-nx = 0
> > fourier-ny = 0
> > fourier-nz = 0
> > pme-order = 4
> > ewald-rtol = 1e-05
> > ewald-rtol-lj = 0.001
> > lj-pme-comb-rule = Geometric
> > ewald-geometry = 0
> > epsilon-surface = 0
> > tcoupl = Nose-Hoover
> > nsttcouple = 15
> > nh-chain-length = 1
> > print-nose-hoover-chain-variables = false
> > pcoupl = No
> > pcoupltype = Isotropic
> > nstpcouple = -1
> > tau-p = 1
> > compressibility (3x3):
> > compressibility[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > compressibility[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > compressibility[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > ref-p (3x3):
> > ref-p[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > ref-p[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > ref-p[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > refcoord-scaling = No
> > posres-com (3):
> > posres-com[0]= 0.00000e+00
> > posres-com[1]= 0.00000e+00
> > posres-com[2]= 0.00000e+00
> > posres-comB (3):
> > posres-comB[0]= 0.00000e+00
> > posres-comB[1]= 0.00000e+00
> > posres-comB[2]= 0.00000e+00
> > QMMM = false
> > QMconstraints = 0
> > QMMMscheme = 0
> > MMChargeScaleFactor = 1
> > qm-opts:
> > ngQM = 0
> > constraint-algorithm = Lincs
> > continuation = false
> > Shake-SOR = false
> > shake-tol = 0.0001
> > lincs-order = 4
> > lincs-iter = 1
> > lincs-warnangle = 30
> > nwall = 0
> > wall-type = 9-3
> > wall-r-linpot = -1
> > wall-atomtype[0] = -1
> > wall-atomtype[1] = -1
> > wall-density[0] = 0
> > wall-density[1] = 0
> > wall-ewald-zfac = 3
> > pull = false
> > awh = false
> > rotation = false
> > interactiveMD = false
> > disre = No
> > disre-weighting = Conservative
> > disre-mixed = false
> > dr-fc = 1000
> > dr-tau = 0
> > nstdisreout = 100
> > orire-fc = 0
> > orire-tau = 0
> > nstorireout = 100
> > free-energy = no
> > cos-acceleration = 0
> > deform (3x3):
> > deform[0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > deform[1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > deform[2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
> > simulated-tempering = false
> > swapcoords = no
> > userint1 = 0
> > userint2 = 0
> > userint3 = 0
> > userint4 = 0
> > userreal1 = 0
> > userreal2 = 0
> > userreal3 = 0
> > userreal4 = 0
> > applied-forces:
> > electric-field:
> > x:
> > E0 = 0
> > omega = 0
> > t0 = 0
> > sigma = 0
> > y:
> > E0 = 0
> > omega = 0
> > t0 = 0
> > sigma = 0
> > z:
> > E0 = 0
> > omega = 0
> > t0 = 0
> > sigma = 0
> > density-guided-simulation:
> > active = false
> > group = protein
> > similarity-measure = inner-product
> > atom-spreading-weight = unity
> > force-constant = 1e+09
> > gaussian-transform-spreading-width = 0.2
> > gaussian-transform-spreading-range-in-multiples-of-width = 4
> > reference-density-filename = reference.mrc
> > nst = 1
> > normalize-densities = true
> > adaptive-force-scaling = false
> > adaptive-force-scaling-time-constant = 4
> > grpopts:
> > nrdf: 3597
> > ref-t: 1100
> > tau-t: 7.5
> > annealing: No
> > annealing-npoints: 0
> > acc: 0 0 0
> > nfreeze: N N N
> > energygrp-flags[0]: 0
> >
> > Changing nstlist from 15 to 25, rlist from 1.14 to 1.288
> >
> > Using 1 MPI thread
> > Using 1 OpenMP thread
> >
> > System total charge: 0.000
> > Reaction-Field:
> > epsRF = 0, rc = 1.1, krf = 0.375657, crf = 1.36364, epsfac = 9.26236
> > The electrostatics potential has its minimum at r = 1.1
> > Potential shift: LJ r^-12: -3.186e-01 r^-6: -5.645e-01
> >
> > Using SIMD 4x8 nonbonded short-range kernels
> >
> > Using a dual 4x8 pair-list setup updated with dynamic pruning:
> > outer list: updated every 25 steps, buffer 0.188 nm, rlist 1.288 nm
> > inner list: updated every 12 steps, buffer 0.004 nm, rlist 1.104 nm
> > At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be:
> > outer list: updated every 25 steps, buffer 0.309 nm, rlist 1.409 nm
> > inner list: updated every 12 steps, buffer 0.038 nm, rlist 1.138 nm
> >
> > Using full Lennard-Jones parameter combination matrix
> >
> > Removing pbc first time
> >
> > Initializing LINear Constraint Solver
> >
> > ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
> > B. Hess
> > P-LINCS: A Parallel Linear Constraint Solver for molecular simulation
> > J. Chem. Theory Comput. 4 (2008) pp. 116-122
> > -------- -------- --- Thank You --- -------- --------
> >
> > The number of constraints is 1200
> > 1200 constraints are involved in constraint triangles,
> > will apply an additional matrix expansion of order 4 for couplings
> > between constraints inside triangles
> > There are: 1600 Atoms
> >
> > Constraining the starting coordinates (step 0)
> >
> > Constraining the coordinates at t0-dt (step 0)
> > Center of mass motion removal mode is Linear
> > We have the following groups for center of mass motion removal:
> > 0: rest
> > RMS relative constraint deviation after constraining: 7.54e-05
> > Initial temperature: 1090.08 K
> >
> > Started mdrun on rank 0 Sat Sep 5 22:23:10 2020
> >
> > Step Time
> > 0 0.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.64324e+03 9.05137e+03 -1.53217e+04 0.00000e+00 -2.62704e+03
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.72719e+04 1.46448e+04 1.46448e+04 1.15503e+03 5.86379e+00
> > Constr. rmsd
> > 9.28210e-05
> >
> > Step Time
> > 1000 25.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.80784e+03 9.45180e+03 -1.34943e+04 0.00000e+00 -2.34628e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.66919e+04 1.64573e+04 1.65240e+04 1.11625e+03 4.91032e-02
> > Constr. rmsd
> > 7.92840e-05
> >
> > Step Time
> > 2000 50.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 4.00155e+03 1.01269e+04 -1.38071e+04 0.00000e+00 3.21352e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.66303e+04 1.69516e+04 1.84123e+04 1.11213e+03 -1.64323e+00
> > Constr. rmsd
> > 7.85634e-05
> >
> > Step Time
> > 3000 75.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.71608e+03 9.59209e+03 -1.42468e+04 0.00000e+00 -9.38593e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.62156e+04 1.52770e+04 2.05502e+04 1.08440e+03 6.30861e+00
> > Constr. rmsd
> > 6.82540e-05
> >
> > Step Time
> > 4000 100.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.88126e+03 8.69774e+03 -1.35513e+04 0.00000e+00 -9.72317e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.60670e+04 1.50947e+04 2.18651e+04 1.07446e+03 -2.76543e+00
> > Constr. rmsd
> > 7.09941e-05
> >
> > Step Time
> > 5000 125.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.81777e+03 9.50289e+03 -1.40430e+04 0.00000e+00 -7.22356e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.64357e+04 1.57133e+04 2.33367e+04 1.09911e+03 3.61202e+00
> > Constr. rmsd
> > 6.84536e-05
> >
> > Step Time
> > 6000 150.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.30286e+03 9.09690e+03 -1.42401e+04 0.00000e+00 -1.84039e+03
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.55963e+04 1.37559e+04 2.47662e+04 1.04298e+03 2.29343e+00
> > Constr. rmsd
> > 5.93324e-05
> >
> > Step Time
> > 7000 175.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 4.05758e+03 9.57547e+03 -1.36260e+04 0.00000e+00 7.05859e+00
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.70971e+04 1.71042e+04 2.67027e+04 1.14335e+03 2.87823e+00
> > Constr. rmsd
> > 7.62672e-05
> >
> > Step Time
> > 8000 200.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.81579e+03 9.49570e+03 -1.35998e+04 0.00000e+00 -2.88294e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.70153e+04 1.67270e+04 2.83461e+04 1.13788e+03 3.68378e+00
> > Constr. rmsd
> > 6.68831e-05
> >
> > Step Time
> > 9000 225.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.68385e+03 9.30925e+03 -1.41326e+04 0.00000e+00 -1.13946e+03
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.48368e+04 1.36973e+04 2.93507e+04 9.92190e+02 -4.02677e-01
> > Constr. rmsd
> > 6.09615e-05
> >
> > Step Time
> > 10000 250.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.61714e+03 9.23332e+03 -1.33140e+04 0.00000e+00 -4.63544e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.63916e+04 1.59281e+04 3.14303e+04 1.09617e+03 -9.91863e-01
> > Constr. rmsd
> > 7.32722e-05
> >
> > Step Time
> > 11000 275.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.84292e+03 9.68248e+03 -1.42625e+04 0.00000e+00 -7.37046e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.68069e+04 1.60698e+04 3.26067e+04 1.12394e+03 1.22513e+00
> > Constr. rmsd
> > 7.29358e-05
> >
> > Step Time
> > 12000 300.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.49386e+03 9.77930e+03 -1.35167e+04 0.00000e+00 -2.43536e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.69808e+04 1.67372e+04 3.41957e+04 1.13557e+03 5.08308e-01
> > Constr. rmsd
> > 8.42676e-05
> >
> > Step Time
> > 13000 325.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.81249e+03 1.00225e+04 -1.40751e+04 0.00000e+00 -2.40137e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.64656e+04 1.62255e+04 3.50788e+04 1.10111e+03 2.09514e+00
> > Constr. rmsd
> > 7.72423e-05
> >
> > Step Time
> > 14000 350.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.90290e+03 9.63802e+03 -1.33045e+04 0.00000e+00 2.36391e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.64963e+04 1.67327e+04 3.70276e+04 1.10317e+03 -1.32518e+00
> > Constr. rmsd
> > 6.95933e-05
> >
> > Step Time
> > 15000 375.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.52809e+03 9.54269e+03 -1.39524e+04 0.00000e+00 -8.81652e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.69839e+04 1.61023e+04 3.89582e+04 1.13578e+03 5.31376e+00
> > Constr. rmsd
> > 9.65680e-05
> >
> > Step Time
> > 16000 400.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.90438e+03 9.70022e+03 -1.41848e+04 0.00000e+00 -5.80218e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.58456e+04 1.52653e+04 4.02027e+04 1.05965e+03 -4.10030e+00
> > Constr. rmsd
> > 7.57252e-05
> >
> > Step Time
> > 17000 425.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.54855e+03 9.51503e+03 -1.35304e+04 0.00000e+00 -4.66862e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.64233e+04 1.59564e+04 4.16487e+04 1.09829e+03 2.81931e-01
> > Constr. rmsd
> > 6.42052e-05
> >
> > Step Time
> > 18000 450.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.48966e+03 9.22245e+03 -1.42361e+04 0.00000e+00 -1.52404e+03
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.64753e+04 1.49512e+04 4.29559e+04 1.10176e+03 -1.84941e+00
> > Constr. rmsd
> > 7.67903e-05
> >
> > Step Time
> > 19000 475.00000
> >
> > Energies (kJ/mol)
> > Bond Angle LJ (SR) Coulomb (SR) Potential
> > 3.52857e+03 9.64361e+03 -1.35359e+04 0.00000e+00 -3.63673e+02
> > Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
> > 1.62009e+04 1.58373e+04 4.41334e+04 1.08342e+03 -2.67067e+00
> > Constr. rmsd
> > 7.07023e-05
> >
> > Constraint error in algorithm Lincs at step 19537
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 19538
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 19539
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 19540
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 19541
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 19542
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 19543
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 19544
> > Wrote pdb files with previous and current coordinates
> > Constraint error in algorithm Lincs at step 19545
> > Wrote pdb files with previous and current coordinates
> >
> > -------------------------------------------------------
> > Program: gmx mdrun, version 2020.3
> > Source file: src/gromacs/mdlib/sim_util.cpp (line 465)
> >
> > Fatal error:
> > Step 19600: The total potential energy is nan, which is not finite. The LJ and
> > electrostatic contributions to the energy are 0 and 0, respectively. A
> > non-finite potential energy can be caused by overlapping interactions in
> > bonded interactions or very large or Nan coordinate values. Usually this is
> > caused by a badly- or non-equilibrated initial configuration, incorrect
> > interactions or parameters in the topology.
> >
> > For more information and tips for troubleshooting, please check the GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> > -------------------------------------------------------
>
> ```
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [September 6, 2020, 6:25pm UTC](https://gromacs.bioexcel.eu/t/lincs-warnings/775/3 "2020-09-06T18:25:15Z")
> [@kw24](#):
>
> `dt = 0.025`
There’s no way the simulation will be stable at high temperature with such a large time step.
---
### Author:  [@kw24](https://gromacs.bioexcel.eu/u/kw24)
#### Post date: [September 6, 2020, 7:53pm UTC](https://gromacs.bioexcel.eu/t/lincs-warnings/775/4 "2020-09-06T19:53:18Z")
Hi Dr. Lemkul,
Thanks for responding! I’m using MARTINI coarse graining, so would that be more acceptable?
---
### Author:  [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)
#### Post date: [September 7, 2020, 1:24am UTC](https://gromacs.bioexcel.eu/t/lincs-warnings/775/5 "2020-09-07T01:24:39Z")
I would still start by reducing `dt`. Force fields are generally parametrized to be used at ambient temperatures and most are not validated at high temperature. In general, **any** high-temperature MD simulation requires a reduced value of `dt` because bond oscillations become more extreme, which can lead to failure.
---
### Author:  [@kw24](https://gromacs.bioexcel.eu/u/kw24)
#### Post date: [September 11, 2020, 3:34am UTC](https://gromacs.bioexcel.eu/t/lincs-warnings/775/6 "2020-09-11T03:34:59Z")
Thank you Dr. Lemkul!
---
### Author:  [@HenriqueBarros](https://gromacs.bioexcel.eu/u/HenriqueBarros)
#### Post date: [December 9, 2021, 12:23pm UTC](https://gromacs.bioexcel.eu/t/lincs-warnings/775/7 "2021-12-09T12:23:28Z")
kw24, did it work to decrease the dt?
to how much did you decrease?