# I set the MD 10ns,and get 4 frames in the xtc file,is it normal? **URL:** \ **Category:** User discussions\ **Created:** [May 9, 2024, 11:12am UTC](https://gromacs.bioexcel.eu/t/i-set-the-md-10ns-and-get-4-frames-in-the-xtc-file-is-it-normal/9115 "2024-05-09T11:12:09Z")\ **Posts on this page:** 12\ **Page:** 1
**Author:** ![ZhangYi](https://avatars.discourse-cdn.com/v4/letter/z/a587f6/32.png) [@ZhangYi](https://gromacs.bioexcel.eu/u/ZhangYi)\ **Post date:** [May 9, 2024, 11:12am UTC](https://gromacs.bioexcel.eu/t/i-set-the-md-10ns-and-get-4-frames-in-the-xtc-file-is-it-normal/9115/1 "2024-05-09T11:12:09Z")
GROMACS version: GROMACS modification: Yes/No Here post your question I set the MD 10ns,and get 4 frames in the xtc file,is it normal? I check the process. Checking file md\_0\_10.xtc Reading frame 0 time 0.000 # Atoms 51659 Precision 0.001 (nm) Last frame 3 time 30.000 Item #frames Timestep (ps) Step 4 10 Time 4 10 Lambda 0 Coords 4 10 Velocities 0 Forces 0 Box 4 10 what does it mean? ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [May 9, 2024, 11:24am UTC](https://gromacs.bioexcel.eu/t/i-set-the-md-10ns-and-get-4-frames-in-the-xtc-file-is-it-normal/9115/2 "2024-05-09T11:24:11Z")
The answer to your question is yes, it can be normal that you get 4 frames in the xtc file if you run for 10 ns. It all depends on the interval you write to the xtc file. However, the output you show below is 4 frames with 10 ps interval, ending at 30 ps. So, that does not match your intention to simulate for 10 ns. Without more information we cannot say what is wrong. ---
**Author:** ![ZhangYi](https://avatars.discourse-cdn.com/v4/letter/z/a587f6/32.png) [@ZhangYi](https://gromacs.bioexcel.eu/u/ZhangYi)\ **Post date:** [May 9, 2024, 11:36am UTC](https://gromacs.bioexcel.eu/t/i-set-the-md-10ns-and-get-4-frames-in-the-xtc-file-is-it-normal/9115/3 "2024-05-09T11:36:01Z")
What information do you need? ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [May 9, 2024, 12:01pm UTC](https://gromacs.bioexcel.eu/t/i-set-the-md-10ns-and-get-4-frames-in-the-xtc-file-is-it-normal/9115/4 "2024-05-09T12:01:00Z")
A good start would be your .mdp file and the .log file from the simulation that produced the 30 ps trajectory, instead of 10 ns, as you had expected. Upload the files somewhere and provide links to them, please. ---
**Author:** ![ZhangYi](https://avatars.discourse-cdn.com/v4/letter/z/a587f6/32.png) [@ZhangYi](https://gromacs.bioexcel.eu/u/ZhangYi)\ **Post date:** [May 9, 2024, 12:18pm UTC](https://gromacs.bioexcel.eu/t/i-set-the-md-10ns-and-get-4-frames-in-the-xtc-file-is-it-normal/9115/5 "2024-05-09T12:18:15Z")
Sorry that I don’t know where to upload,so I copy the two file md.mdp 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\_3TE 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 md\_0\_10.log ++++ PLEASE CITE THE DOI FOR THIS VERSION OF GROMACS ++++ > **[GROMACS 2022.2 Source code](https://zenodo.org/records/6637571)** > > Source code archive of the 2022.2 patch version of GROMACS. -------- -------- — Thank You — -------- -------- Input Parameters: integrator = md tinit = 0 dt = 0.002 nsteps = 5000000 init-step = 0 simulation-part = 1 mts = false comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = 2006896589 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 5000 nstcalcenergy = 100 nstenergy = 5000 nstxout-compressed = 5000 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 20 pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 1.222 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1.2 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Force-switch rvdw-switch = 1 rvdw = 1.2 DispCorr = No table-extension = 1 fourierspacing = 0.16 fourier-nx = 56 fourier-ny = 56 fourier-nz = 56 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 3d epsilon-surface = 0 tcoupl = V-rescale nsttcouple = 10 nh-chain-length = 0 print-nose-hoover-chain-variables = false pcoupl = Parrinello-Rahman pcoupltype = Isotropic nstpcouple = 10 tau-p = 2 compressibility (3x3): compressibility[0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} compressibility[1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} compressibility[2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} ref-p (3x3): ref-p[0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} ref-p[2]={ 0.00000e+00, 0.00000e+00, 1.00000e+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 qm-opts: ngQM = 0 constraint-algorithm = Lincs continuation = true 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 shift-vector = transformation-matrix = qmmm-cp2k: active = false qmgroup = System qmmethod = PBE qmfilenames = qmcharge = 0 qmmultiplicity = 1 grpopts: nrdf: 11739.7 93939.3 ref-t: 300 300 tau-t: 0.1 0.1 annealing: No No annealing-npoints: 0 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[0]: 0 Changing nstlist from 20 to 80, rlist from 1.222 to 1.319 When checking whether update groups are usable: At least one moleculetype does not conform to the requirements for using update groups Initializing Domain Decomposition on 56 ranks Dynamic load balancing: auto Minimum cell size due to atom displacement: 0.644 nm Initial maximum distances in bonded interactions: two-body bonded interactions: 0.433 nm, LJ-14, atoms 3256 3264 multi-body bonded interactions: 0.495 nm, CMAP Dih., atoms 3842 3851 Minimum cell size due to bonded interactions: 0.545 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.222 nm Estimated maximum distance required for P-LINCS: 0.222 nm Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Guess for relative PME load: 0.12 Will use 49 particle-particle and 7 PME only ranks This is a guess, check the performance at the end of the log file Using 7 separate PME ranks, as guessed by mdrun Optimizing the DD grid for 49 cells with a minimum initial size of 0.805 nm The maximum allowed number of cells is: X 9 Y 9 Z 7 Domain decomposition grid 7 x 7 x 1, separate PME ranks 7 PME domain decomposition: 7 x 1 x 1 Interleaving PP and PME ranks This rank does only particle-particle work. Domain decomposition rank 0, coordinates 0 0 0 The initial number of communication pulses is: X 2 Y 2 The initial domain decomposition cell size is: X 1.04 nm Y 1.04 nm The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.319 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.319 nm multi-body bonded interactions (-rdd) 1.044 nm atoms separated by up to 5 constraints (-rcon) 1.044 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 2 Y 2 The minimum size for domain decomposition cells is 0.794 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.76 Y 0.76 The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.319 nm two-body bonded interactions (-rdd) 1.319 nm multi-body bonded interactions (-rdd) 0.794 nm atoms separated by up to 5 constraints (-rcon) 0.794 nm Using 56 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process System total charge: 0.000 Will do PME sum in reciprocal space for electrostatic interactions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- — Thank You — -------- -------- Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Potential shift: LJ r^-12: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06 Initialized non-bonded Coulomb Ewald tables, spacing: 1.02e-03 size: 1176 Generated table with 1159 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1159 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1159 data points for 1-4 LJ12. Tabscale = 500 points/nm Using SIMD 4x8 nonbonded short-range kernels Using a dual 4x8 pair-list setup updated with dynamic pruning: outer list: updated every 80 steps, buffer 0.119 nm, rlist 1.319 nm inner list: updated every 13 steps, buffer 0.001 nm, rlist 1.201 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 80 steps, buffer 0.263 nm, rlist 1.463 nm inner list: updated every 13 steps, buffer 0.051 nm, rlist 1.251 nm Linking all bonded interactions to atoms ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [May 9, 2024, 12:27pm UTC](https://gromacs.bioexcel.eu/t/i-set-the-md-10ns-and-get-4-frames-in-the-xtc-file-is-it-normal/9115/6 "2024-05-09T12:27:40Z")
There is nothing apparently wrong with the settings. I can set two alternatives, the simulation crashed after 30 ps (you didn’t include the whole log file, so it’s impossible to say) or the trajectory file was from another simulation. ---
**Author:** ![ZhangYi](https://avatars.discourse-cdn.com/v4/letter/z/a587f6/32.png) [@ZhangYi](https://gromacs.bioexcel.eu/u/ZhangYi)\ **Post date:** [May 9, 2024, 12:31pm UTC](https://gromacs.bioexcel.eu/t/i-set-the-md-10ns-and-get-4-frames-in-the-xtc-file-is-it-normal/9115/7 "2024-05-09T12:31:39Z")
This is all the log file. :-) GROMACS - gmx mdrun, 2022.2-dev (-: Copyright 1991-2022 The GROMACS Authors. GROMACS is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. ``` Current GROMACS contributors: Mark Abraham Andrey Alekseenko Cathrine Bergh Christian Blau Eliane Briand Kevin Boyd Oliver Fleetwood Stefan Fleischmann Vytas Gapsys Gaurav Garg Gilles Gouaillardet Alan Gray Victor Holanda M. Eric Irrgang Joe Jordan Christoph Junghans Prashanth Kanduri Sebastian Kehl Sebastian Keller Carsten Kutzner Magnus Lundborg Pascal Merz Dmitry Morozov Szilard Pall Roland Schulz Michael Shirts David van der Spoel Alessandra Villa Sebastian Wingbermuehle Artem Zhmurov Previous GROMACS contributors: Emile Apol Rossen Apostolov James Barnett ``` Herman J.C. Berendsen Par Bjelkmar Viacheslav Bolnykh Aldert van Buuren Carlo Camilloni Rudi van Drunen Anton Feenstra Gerrit Groenhof Bert de Groot Anca Hamuraru Vincent Hindriksen Aleksei Iupinov Dimitrios Karkoulis Peter Kasson Jiri Kraus Per Larsson Justin A. Lemkul Viveca Lindahl Erik Marklund Pieter Meulenhoff Vedran Miletic Teemu Murtola Sander Pronk Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf ``` Coordinated by the GROMACS project leaders: Paul Bauer, Berk Hess, and Erik Lindahl ``` GROMACS: gmx mdrun, version 2022.2-dev Executable: /es01/paratera/parasoft/gromacs-2022.2/install/bin/gmx\_mpi Data prefix: /es01/paratera/parasoft/gromacs-2022.2/install Working dir: /es01/paratera/sce2008/4RMH Process ID: 181180 Command line: gmx\_mpi mdrun -deffnm md\_0\_10 GROMACS version: 2022.2-dev Precision: mixed Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX\_OPENMP\_MAX\_THREADS = 128) GPU support: disabled SIMD instructions: AVX2\_256 CPU FFT library: fftw-3.3.8-sse2-avx-avx2-avx2\_128 GPU FFT library: none RDTSCP usage: enabled TNG support: enabled Hwloc support: disabled Tracing support: disabled C compiler: /es01/software/intel2020/compilers\_and\_libraries\_2020.4.304/linux/mpi/intel64/bin/mpicc GNU 8.3.0 C compiler flags: -mavx2 -mfma -Wall -Wno-unused -Wunused-value -Wunused-parameter -Wextra -Wno-sign-compare -Wpointer-arith -Wundef -Werror=stringop-truncation -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-array-bounds -O3 -DNDEBUG C++ compiler: /es01/software/intel2020/compilers\_and\_libraries\_2020.4.304/linux/mpi/intel64/bin/mpicxx GNU 8.3.0 C++ compiler flags: -mavx2 -mfma -Wall -Wextra -Wpointer-arith -Wmissing-declarations -Wundef -Wstringop-truncation -Wno-missing-field-initializers -fexcess-precision=fast -funroll-all-loops -Wno-array-bounds -fopenmp -O3 -DNDEBUG Running on 1 node with total 56 cores, 56 processing units Hardware detected on host n02318 (the node of MPI rank 0): CPU info: Vendor: Intel Brand: Intel(R) Xeon(R) Gold 6258R CPU @ 2.70GHz Family: 6 Model: 85 Stepping: 7 Features: aes apic avx avx2 avx512f avx512cd avx512bw avx512vl avx512secondFMA clfsh cmov cx8 cx16 f16c fma hle htt intel lahf mmx msr nonstop\_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic Number of AVX-512 FMA units: 2 Hardware topology: Basic Packages, cores, and logical processors: [indices refer to OS logical processors] Package 0: [0] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] Package 1: [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] CPU limit set by OS: -1 Recommended max number of threads: 56 Highest SIMD level supported by all nodes in run: AVX\_512 SIMD instructions selected at compile time: AVX2\_256 This program was compiled for different hardware than you are running on, which could influence performance. This build might have been configured on a login node with only a single AVX-512 FMA unit (in which case AVX2 is faster), while the node you are running on has dual AVX-512 FMA units. ++++ 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 ++++ > **[GROMACS 2022.2 Source code](https://zenodo.org/records/6637571)** > > Source code archive of the 2022.2 patch version of GROMACS. -------- -------- — Thank You — -------- -------- Input Parameters: integrator = md tinit = 0 dt = 0.002 nsteps = 5000000 init-step = 0 simulation-part = 1 mts = false comm-mode = Linear nstcomm = 100 bd-fric = 0 ld-seed = 2006896589 emtol = 10 emstep = 0.01 niter = 20 fcstep = 0 nstcgsteep = 1000 nbfgscorr = 10 rtpi = 0.05 nstxout = 0 nstvout = 0 nstfout = 0 nstlog = 5000 nstcalcenergy = 100 nstenergy = 5000 nstxout-compressed = 5000 compressed-x-precision = 1000 cutoff-scheme = Verlet nstlist = 20 pbc = xyz periodic-molecules = false verlet-buffer-tolerance = 0.005 rlist = 1.222 coulombtype = PME coulomb-modifier = Potential-shift rcoulomb-switch = 0 rcoulomb = 1.2 epsilon-r = 1 epsilon-rf = inf vdw-type = Cut-off vdw-modifier = Force-switch rvdw-switch = 1 rvdw = 1.2 DispCorr = No table-extension = 1 fourierspacing = 0.16 fourier-nx = 56 fourier-ny = 56 fourier-nz = 56 pme-order = 4 ewald-rtol = 1e-05 ewald-rtol-lj = 0.001 lj-pme-comb-rule = Geometric ewald-geometry = 3d epsilon-surface = 0 tcoupl = V-rescale nsttcouple = 10 nh-chain-length = 0 print-nose-hoover-chain-variables = false pcoupl = Parrinello-Rahman pcoupltype = Isotropic nstpcouple = 10 tau-p = 2 compressibility (3x3): compressibility[0]={ 4.50000e-05, 0.00000e+00, 0.00000e+00} compressibility[1]={ 0.00000e+00, 4.50000e-05, 0.00000e+00} compressibility[2]={ 0.00000e+00, 0.00000e+00, 4.50000e-05} ref-p (3x3): ref-p[0]={ 1.00000e+00, 0.00000e+00, 0.00000e+00} ref-p[1]={ 0.00000e+00, 1.00000e+00, 0.00000e+00} ref-p[2]={ 0.00000e+00, 0.00000e+00, 1.00000e+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 qm-opts: ngQM = 0 constraint-algorithm = Lincs continuation = true 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 shift-vector = transformation-matrix = qmmm-cp2k: active = false qmgroup = System qmmethod = PBE qmfilenames = qmcharge = 0 qmmultiplicity = 1 grpopts: nrdf: 11739.7 93939.3 ref-t: 300 300 tau-t: 0.1 0.1 annealing: No No annealing-npoints: 0 0 acc: 0 0 0 nfreeze: N N N energygrp-flags[0]: 0 Changing nstlist from 20 to 80, rlist from 1.222 to 1.319 When checking whether update groups are usable: At least one moleculetype does not conform to the requirements for using update groups Initializing Domain Decomposition on 56 ranks Dynamic load balancing: auto Minimum cell size due to atom displacement: 0.644 nm Initial maximum distances in bonded interactions: two-body bonded interactions: 0.433 nm, LJ-14, atoms 3256 3264 multi-body bonded interactions: 0.495 nm, CMAP Dih., atoms 3842 3851 Minimum cell size due to bonded interactions: 0.545 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.222 nm Estimated maximum distance required for P-LINCS: 0.222 nm Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25 Guess for relative PME load: 0.12 Will use 49 particle-particle and 7 PME only ranks This is a guess, check the performance at the end of the log file Using 7 separate PME ranks, as guessed by mdrun Optimizing the DD grid for 49 cells with a minimum initial size of 0.805 nm The maximum allowed number of cells is: X 9 Y 9 Z 7 Domain decomposition grid 7 x 7 x 1, separate PME ranks 7 PME domain decomposition: 7 x 1 x 1 Interleaving PP and PME ranks This rank does only particle-particle work. Domain decomposition rank 0, coordinates 0 0 0 The initial number of communication pulses is: X 2 Y 2 The initial domain decomposition cell size is: X 1.04 nm Y 1.04 nm The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.319 nm (the following are initial values, they could change due to box deformation) two-body bonded interactions (-rdd) 1.319 nm multi-body bonded interactions (-rdd) 1.044 nm atoms separated by up to 5 constraints (-rcon) 1.044 nm When dynamic load balancing gets turned on, these settings will change to: The maximum number of communication pulses is: X 2 Y 2 The minimum size for domain decomposition cells is 0.794 nm The requested allowed shrink of DD cells (option -dds) is: 0.80 The allowed shrink of domain decomposition cells is: X 0.76 Y 0.76 The maximum allowed distance for atoms involved in interactions is: non-bonded interactions 1.319 nm two-body bonded interactions (-rdd) 1.319 nm multi-body bonded interactions (-rdd) 0.794 nm atoms separated by up to 5 constraints (-rcon) 0.794 nm Using 56 MPI processes Non-default thread affinity set, disabling internal thread affinity Using 1 OpenMP thread per MPI process System total charge: 0.000 Will do PME sum in reciprocal space for electrostatic interactions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee and L. G. Pedersen A smooth particle mesh Ewald method J. Chem. Phys. 103 (1995) pp. 8577-8592 -------- -------- — Thank You — -------- -------- Using a Gaussian width (1/beta) of 0.384195 nm for Ewald Potential shift: LJ r^-12: -2.648e-01 r^-6: -5.349e-01, Ewald -8.333e-06 Initialized non-bonded Coulomb Ewald tables, spacing: 1.02e-03 size: 1176 Generated table with 1159 data points for 1-4 COUL. Tabscale = 500 points/nm Generated table with 1159 data points for 1-4 LJ6. Tabscale = 500 points/nm Generated table with 1159 data points for 1-4 LJ12. Tabscale = 500 points/nm Using SIMD 4x8 nonbonded short-range kernels Using a dual 4x8 pair-list setup updated with dynamic pruning: outer list: updated every 80 steps, buffer 0.119 nm, rlist 1.319 nm inner list: updated every 13 steps, buffer 0.001 nm, rlist 1.201 nm At tolerance 0.005 kJ/mol/ps per atom, equivalent classical 1x1 list would be: outer list: updated every 80 steps, buffer 0.263 nm, rlist 1.463 nm inner list: updated every 13 steps, buffer 0.051 nm, rlist 1.251 nm Linking all bonded interactions to atoms Initializing Parallel 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 2333 There are constraints between atoms in different decomposition domains, will communicate selected coordinates each lincs iteration ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ S. Miyamoto and P. A. Kollman SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithms for Rigid Water Models J. Comp. Chem. 13 (1992) pp. 952-962 -------- -------- — Thank You — -------- -------- Intra-simulation communication will occur every 10 steps. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ G. Bussi, D. Donadio and M. Parrinello Canonical sampling through velocity rescaling J. Chem. Phys. 126 (2007) pp. 014101 -------- -------- — Thank You — -------- -------- There are: 51659 Atoms Atom distribution over 49 domains: av 1054 stddev 35 min 996 max 1122 Center of mass motion removal mode is Linear We have the following groups for center of mass motion removal: 0: rest Started mdrun on rank 0 Thu May 9 00:08:48 2024 ``` Step Time 0 0.00000 ``` Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 3.85695e+03 1.08233e+04 1.24223e+04 6.64243e+02 -3.68648e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 4.02752e+03 5.04419e+04 6.03038e+04 -8.10621e+05 2.51307e+03 Potential Kinetic En. Total Energy Conserved En. Temperature -6.65937e+05 1.31726e+05 -5.34210e+05 -5.34180e+05 2.99833e+02 Pressure (bar) Constr. rmsd 2.85752e+01 3.33859e-06 DD step 79 load imb.: force 11.6% pme mesh/force 0.492 step 240 Turning on dynamic load balancing, because the performance loss due to load imbalance is 5.6 %. Step Time 5000 10.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 3.95122e+03 1.09889e+04 1.23460e+04 6.18268e+02 -4.50679e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 3.80860e+03 5.02288e+04 6.07906e+04 -8.10765e+05 2.42138e+03 Potential Kinetic En. Total Energy Conserved En. Temperature -6.66062e+05 1.32096e+05 -5.33966e+05 -5.34083e+05 3.00674e+02 Pressure (bar) Constr. rmsd -4.51211e+01 3.29013e-06 DD step 9999 vol min/aver 0.877 load imb.: force 4.5% pme mesh/force 0.490 Step Time 10000 20.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 3.97649e+03 1.06274e+04 1.23479e+04 6.00813e+02 -4.52109e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 4.06390e+03 5.04673e+04 5.95876e+04 -8.09761e+05 2.44050e+03 Potential Kinetic En. Total Energy Conserved En. Temperature -6.66101e+05 1.31085e+05 -5.35016e+05 -5.33972e+05 2.98373e+02 Pressure (bar) Constr. rmsd -1.63797e+01 2.95202e-06 step 14400 Turning off dynamic load balancing, because it is degrading performance. Atom distribution over 49 domains: av 1054 stddev 31 min 1014 max 1104 Step Time 15000 30.00000 Energies (kJ/mol) Bond U-B Proper Dih. Improper Dih. CMAP Dih. 3.76916e+03 1.09247e+04 1.22990e+04 6.46692e+02 -4.39659e+02 LJ-14 Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. 3.93045e+03 5.02139e+04 6.26199e+04 -8.14065e+05 2.44340e+03 Potential Kinetic En. Total Energy Conserved En. Temperature -6.67657e+05 1.31792e+05 -5.35865e+05 -5.33885e+05 2.99984e+02 Pressure (bar) Constr. rmsd 2.80120e+02 3.16420e-06 ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [May 9, 2024, 12:46pm UTC](https://gromacs.bioexcel.eu/t/i-set-the-md-10ns-and-get-4-frames-in-the-xtc-file-is-it-normal/9115/8 "2024-05-09T12:46:44Z")
Then it’s clear that it stopped or crashed after 30 ps. Hopefully there was more information in the terminal or the run log - depending on how the job was started. But I’d suspect that your system has exploded. There are many threads about that on this forum. ---
**Author:** ![ZhangYi](https://avatars.discourse-cdn.com/v4/letter/z/a587f6/32.png) [@ZhangYi](https://gromacs.bioexcel.eu/u/ZhangYi)\ **Post date:** [May 9, 2024, 12:49pm UTC](https://gromacs.bioexcel.eu/t/i-set-the-md-10ns-and-get-4-frames-in-the-xtc-file-is-it-normal/9115/9 "2024-05-09T12:49:02Z")
OK.Thank you very much! I will sreach for more information then. ---
**Author:** ![ZhangYi](https://avatars.discourse-cdn.com/v4/letter/z/a587f6/32.png) [@ZhangYi](https://gromacs.bioexcel.eu/u/ZhangYi)\ **Post date:** [May 9, 2024, 12:52pm UTC](https://gromacs.bioexcel.eu/t/i-set-the-md-10ns-and-get-4-frames-in-the-xtc-file-is-it-normal/9115/10 "2024-05-09T12:52:16Z")
Can you predict which step caused this explosion? I have seen so many reasons but can’t conform which one. ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [May 10, 2024, 8:20am UTC](https://gromacs.bioexcel.eu/t/i-set-the-md-10ns-and-get-4-frames-in-the-xtc-file-is-it-normal/9115/11 "2024-05-10T08:20:17Z")
The first thing I’d do is to check if the system is equilibrated well enough. I’d run a shorter simulation before the long one. In the short simulation I would run with: ```auto dt = 0.001 nsteps = 250000 define = -DPOSRES ``` In both the short and the longer simulations I would run with: ```auto tau_t = 0.5 0.5 pcoupl = c-rescale tau_p = 5.0 ``` Parrinello-Rahman barostat with a short coupling time is often causing crashes. Hopefully that will help or at least give more insight. ---
**Author:** ![ZhangYi](https://avatars.discourse-cdn.com/v4/letter/z/a587f6/32.png) [@ZhangYi](https://gromacs.bioexcel.eu/u/ZhangYi)\ **Post date:** [May 10, 2024, 12:40pm UTC](https://gromacs.bioexcel.eu/t/i-set-the-md-10ns-and-get-4-frames-in-the-xtc-file-is-it-normal/9115/12 "2024-05-10T12:40:12Z")
OK! Thank you very much! I will try again!