:-) GROMACS - gmx grompp, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. 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. GROMACS: gmx grompp, version 2019.1 Executable: /usr/local/tools/_conda/envs/__gromacs@2019.1/bin/gmx Data prefix: /usr/local/tools/_conda/envs/__gromacs@2019.1 Working dir: /data/dnb02/galaxy_db/job_working_directory/008/462/8462118/working Command line: gmx grompp -f ./md.mdp -c ./inp.gro -r ./inp.gro -p ./top_input.top -o outp.tpr Ignoring obsolete mdp entry 'title' Setting the LD random seed to -1425965266 Generated 2926 of the 2926 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2926 of the 2926 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'base' Excluding 2 bonded neighbours molecule type 'SOL' Excluding 1 bonded neighbours molecule type 'NA' NOTE 1 [file unknown]: You are using constraints on all bonds, whereas the forcefield has been parametrized only with constraints involving hydrogen atoms. We suggest using constraints = h-bonds instead, this will also improve performance. Removing all charge groups because cutoff-scheme=Verlet The center of mass of the position restraint coord's is 3.248 3.226 3.199 The center of mass of the position restraint coord's is 3.248 3.226 3.199 Number of degrees of freedom in T-Coupling group Protein is 6533.63 Number of degrees of freedom in T-Coupling group non-Protein is 46179.37 Estimate for the relative computational load of the PME mesh part: 0.15 There was 1 note GROMACS reminds you: "I've basically become a vegetarian since the only meat I'm eating is from animals I've killed myself" (Mark Zuckerberg) turning all bonds into constraints... turning all bonds into constraints... turning all bonds into constraints... turning all bonds into constraints... Analysing residue names: There are: 208 Protein residues There are: 1 Other residues There are: 7684 Water residues There are: 6 Ion residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K Calculated rlist for 1x1 atom pair-list as 1.033 nm, buffer size 0.033 nm Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm Note that mdrun will redetermine rlist based on the actual pair-list setup Calculating fourier grid dimensions for X Y Z Using a fourier grid of 42x42x42, spacing 0.154 0.154 0.153 This run will generate roughly 39 Mb of data :-) GROMACS - gmx mdrun, 2019.1 (-: GROMACS is written by: Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen Christian Wennberg Maarten Wolf and the project leaders: Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel Copyright (c) 1991-2000, University of Groningen, The Netherlands. Copyright (c) 2001-2018, The GROMACS development team at Uppsala University, Stockholm University and the Royal Institute of Technology, Sweden. check out http://www.gromacs.org for more information. 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. GROMACS: gmx mdrun, version 2019.1 Executable: /usr/local/tools/_conda/envs/__gromacs@2019.1/bin/gmx Data prefix: /usr/local/tools/_conda/envs/__gromacs@2019.1 Working dir: /data/dnb02/galaxy_db/job_working_directory/008/462/8462118/working Command line: gmx mdrun -nt 16 -deffnm outp Compiled SIMD: SSE2, but for this host/run AVX2_256 might be better (see log). The current CPU can measure timings more accurately than the code in gmx mdrun was configured to use. This might affect your simulation speed as accurate timings are needed for load-balancing. Please consider rebuilding gmx mdrun with the GMX_USE_RDTSCP=ON CMake option. Reading file outp.tpr, VERSION 2019.1 (single precision) Changing nstlist from 10 to 50, rlist from 1 to 1.102 Using 1 MPI thread Using 16 OpenMP threads NOTE: The number of threads is not equal to the number of (logical) cores and the -pin option is set to auto: will not pin threads to cores. This can lead to significant performance degradation. Consider using -pin on (and -pinoffset in case you run multiple jobs). starting mdrun 'HEAT SHOCK PROTEIN HSP 90-ALPHA' 50000 steps, 100.0 ps. Writing final coordinates. Core t (s) Wall t (s) (%) Time: 5045.807 315.373 1599.9 (ns/day) (hour/ns) Performance: 27.397 0.876 GROMACS reminds you: "O My God, They Killed Kenny !" (South Park) title = OPLS Lysozyme MD simulation ; Run parameters integrator = md ; leap-frog integrator nsteps = 50000 ; 2 * 500000 = 1000 ps (1 ns) dt = 0.002 ; 2 fs ; Output control nstxout = 1000 ; save coordinates every 10.0 ps nstvout = 1000 ; save velocities every 10.0 ps nstenergy = 1000 ; save energies every 10.0 ps nstlog = 1000 ; update log file every 10.0 ps nstxout-compressed = 1000 ; save compressed coordinates every 10.0 ps ; nstxout-compressed replaces nstxtcout compressed-x-grps = System ; group(s) to write to the compressed trajectory file ; Bond parameters constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching cutoff-scheme = Verlet ns_type = grid ; search neighboring grid cells nstlist = 10 ; 20 fs, largely irrelevant with Verlet scheme rcoulomb = 1.0 ; Short-range electrostatic cut-off rlist = 1.0 ; Cut-off distance for the short-range neighbor list. rvdw = 1.0 ; Short-range Van der Waals cut-off ; Electrostatics coulombtype = PME ; method for electrostatics calculations e.g. PME 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 ; 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 define = -DPOSRES ; position restrain the protein refcoord_scaling = com pcoupl = no ; no pressure coupling in NVT