:-) GROMACS - gmx solvate, 2020.4 (-: 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 Artem Zhmurov 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) 2001-2019, 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 solvate, version 2020.4 Executable: /usr/local/tools/_conda/envs/__gromacs@2020.4/bin.AVX2_256/gmx Data prefix: /usr/local/tools/_conda/envs/__gromacs@2020.4 Working dir: /data/dnb03/galaxy_db/job_working_directory/024/447/24447726/working Command line: gmx solvate -cp ./gro_input.gro -cs spc216.gro -o solv.gro -p ./top_input.top Reading solute configuration Reading solvent configuration Initialising inter-atomic distances... WARNING: Masses and atomic (Van der Waals) radii will be guessed based on residue and atom names, since they could not be definitively assigned from the information in your input files. These guessed numbers might deviate from the mass and radius of the atom type. Please check the output files if necessary. NOTE: From version 5.0 gmx solvate uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Generating solvent configuration Will generate new solvent configuration of 4x4x4 boxes Solvent box contains 30576 atoms in 10192 residues Removed 4338 solvent atoms due to solvent-solvent overlap Removed 3168 solvent atoms due to solute-solvent overlap Sorting configuration Found 1 molecule type: SOL ( 3 atoms): 7690 residues Generated solvent containing 23070 atoms in 7690 residues Writing generated configuration to solv.gro Output configuration contains 26381 atoms in 7899 residues Volume : 268.205 (nm^3) Density : 1013.54 (g/l) Number of solvent molecules: 7690 Processing topology Back Off! I just backed up ./top_input.top to ./#top_input.top.1# GROMACS reminds you: "Does All This Money Really Have To Go To Charity ?" (Rick) Adding line for 7690 solvent molecules with resname (SOL) to topology file (./top_input.top) :-) GROMACS - gmx grompp, 2020.4 (-: 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 Artem Zhmurov 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) 2001-2019, 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 2020.4 Executable: /usr/local/tools/_conda/envs/__gromacs@2020.4/bin.AVX2_256/gmx Data prefix: /usr/local/tools/_conda/envs/__gromacs@2020.4 Working dir: /data/dnb03/galaxy_db/job_working_directory/024/447/24447726/working Command line: gmx grompp -f ./ions.mdp -c solv.gro -p ./top_input.top -o ions.tpr Ignoring obsolete mdp entry 'ns_type' NOTE 1 [file ./ions.mdp]: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation. Setting the LD random seed to -1505639592 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' NOTE 2 [file top_input.top, line 31164]: System has non-zero total charge: -6.000000 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. Number of degrees of freedom in T-Coupling group rest is 56070.00 NOTE 3 [file ./ions.mdp]: You are using a plain Coulomb cut-off, which might produce artifacts. You might want to consider using PME electrostatics. There were 3 notes GROMACS reminds you: "Developing the AI requires the work of a data scientist, and most of them understand neither data nor science." (Scott LeGrand) Analysing residue names: There are: 208 Protein residues There are: 1 Other residues There are: 7690 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... This run will generate roughly 2 Mb of data :-) GROMACS - gmx genion, 2020.4 (-: 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 Artem Zhmurov 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) 2001-2019, 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 genion, version 2020.4 Executable: /usr/local/tools/_conda/envs/__gromacs@2020.4/bin.AVX2_256/gmx Data prefix: /usr/local/tools/_conda/envs/__gromacs@2020.4 Working dir: /data/dnb03/galaxy_db/job_working_directory/024/447/24447726/working Command line: gmx genion -s ions.tpr -o solv_ions.gro -p ./top_input.top -pname NA -nname CL -neutral -conc 0.0 Reading file ions.tpr, VERSION 2020.4 (single precision) Reading file ions.tpr, VERSION 2020.4 (single precision) Group 0 ( System) has 26381 elements Group 1 ( Protein) has 3280 elements Group 2 ( Protein-H) has 1636 elements Group 3 ( C-alpha) has 208 elements Group 4 ( Backbone) has 624 elements Group 5 ( MainChain) has 833 elements Group 6 ( MainChain+Cb) has 1026 elements Group 7 ( MainChain+H) has 1039 elements Group 8 ( SideChain) has 2241 elements Group 9 ( SideChain-H) has 803 elements Group 10 ( Prot-Masses) has 3280 elements Group 11 ( non-Protein) has 23101 elements Group 12 ( Other) has 31 elements Group 13 ( G5E) has 31 elements Group 14 ( Water) has 23070 elements Group 15 ( SOL) has 23070 elements Group 16 ( non-Water) has 3311 elements Select a group: Number of (3-atomic) solvent molecules: 7690 Back Off! I just backed up ./top_input.top to ./#top_input.top.2# Using random seed -1582034896. Replacing solvent molecule 2249 (atom 10058) with NA Replacing solvent molecule 7351 (atom 25364) with NA Replacing solvent molecule 28 (atom 3395) with NA Replacing solvent molecule 7352 (atom 25367) with NA Replacing solvent molecule 878 (atom 5945) with NA Replacing solvent molecule 5007 (atom 18332) with NA GROMACS reminds you: "These Gromacs Guys Really Rock" (P.J. Meulenhoff) Will try to add 6 NA ions and 0 CL ions. Select a continuous group of solvent molecules Selected 15: 'SOL' Processing topology Replacing 6 solute molecules in topology file (./top_input.top) by 6 NA and 0 CL ions.