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!