Mercurial > repos > agpetit > calculate_diameter
diff test-data/cut_trajectories_file.log @ 4:433dba16af7d draft
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
| author | agpetit |
|---|---|
| date | Fri, 27 May 2022 09:07:29 +0000 |
| parents | c574ada16e76 |
| children | e504457035e5 |
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--- a/test-data/cut_trajectories_file.log Fri May 27 07:36:52 2022 +0000 +++ b/test-data/cut_trajectories_file.log Fri May 27 09:07:29 2022 +0000 @@ -16,45 +16,18 @@ INFO - .gro file is PIP2.1_test.gro INFO - .xtc file is PIP2.1_test.xtc INFO - Output directory is out/ -INFO - The name of .log file is log/cut_trajectories.log +INFO - The name of .log file is out_log/cut_trajectories.log INFO - The number of cpus used is 1 INFO - Sub_trajectory 1 starts at 0 ps and ends at 20 ps INFO - Sub_trajectory 2 starts at 30 ps and ends at 50 ps INFO - Sub_trajectory 3 starts at 60 ps and ends at 80 ps INFO - Launch gmx trjconv - :-) GROMACS - gmx trjconv, 2020.1-Ubuntu-2020.1-1 (-: + :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-: - 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 trjconv, version 2020.1-Ubuntu-2020.1-1 -Executable: /usr/bin/gmx -Data prefix: /usr -Working dir: /home/aepetit/Documents/scripts/Stage-M2/wrapper/test-data +Executable: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1/bin.AVX2_256/gmx +Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1 +Working dir: /tmp/tmp87fei_xs/job_working_directory/000/5/working Command line: gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 0 -e 20 -o out/PIP2.1_test_traj_1.xtc @@ -80,52 +53,26 @@ Reading frame 0 time 0.000 Precision of PIP2.1_test.xtc is 0.001 (nm) Using output precision of 0.001 (nm) - -> frame 0 time 0.000 -Reading frame 1 time 10.000 -> frame 1 time 10.000 +Reading frame 1 time 10.000 -> frame 0 time 0.000 -Reading frame 2 time 20.000 -> frame 2 time 20.000 +Reading frame 2 time 20.000 -> frame 1 time 10.000 Last frame 2 time 20.000 + -> frame 2 time 20.000 +Last written: frame 2 time 20.000 -GROMACS reminds you: "Do You Have Sex Maniacs or Schizophrenics or Astrophysicists in Your Family?" (Gogol Bordello) +GROMACS reminds you: "The Microsecond is Within Reach" (P.J. Van Maaren) Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 0: 'System' - :-) GROMACS - gmx trjconv, 2020.1-Ubuntu-2020.1-1 (-: + :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-: - 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 trjconv, version 2020.1-Ubuntu-2020.1-1 -Executable: /usr/bin/gmx -Data prefix: /usr -Working dir: /home/aepetit/Documents/scripts/Stage-M2/wrapper/test-data +Executable: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1/bin.AVX2_256/gmx +Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1 +Working dir: /tmp/tmp87fei_xs/job_working_directory/000/5/working Command line: gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 30 -e 50 -o out/PIP2.1_test_traj_2.xtc @@ -152,52 +99,26 @@ Reading frame 0 time 30.000 Precision of PIP2.1_test.xtc is 0.001 (nm) Using output precision of 0.001 (nm) - -> frame 0 time 30.000 -Reading frame 1 time 40.000 -> frame 1 time 40.000 +Reading frame 1 time 40.000 -> frame 0 time 30.000 -Reading frame 2 time 50.000 -> frame 2 time 50.000 +Reading frame 2 time 50.000 -> frame 1 time 40.000 Last frame 2 time 50.000 + -> frame 2 time 50.000 +Last written: frame 2 time 50.000 -GROMACS reminds you: "The use of COBOL cripples the mind; its teaching should therefore be regarded as a criminal offense." (Edsger Dijkstra) +GROMACS reminds you: "I'm Not Gonna Die Here !" (Sphere) Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output Selected 0: 'System' - :-) GROMACS - gmx trjconv, 2020.1-Ubuntu-2020.1-1 (-: + :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-: - 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 trjconv, version 2020.1-Ubuntu-2020.1-1 -Executable: /usr/bin/gmx -Data prefix: /usr -Working dir: /home/aepetit/Documents/scripts/Stage-M2/wrapper/test-data +Executable: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1/bin.AVX2_256/gmx +Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1 +Working dir: /tmp/tmp87fei_xs/job_working_directory/000/5/working Command line: gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 60 -e 80 -o out/PIP2.1_test_traj_3.xtc @@ -224,16 +145,17 @@ Reading frame 0 time 60.000 Precision of PIP2.1_test.xtc is 0.001 (nm) Using output precision of 0.001 (nm) - -> frame 0 time 60.000 -Reading frame 1 time 70.000 -> frame 1 time 70.000 +Reading frame 1 time 70.000 -> frame 0 time 60.000 -Reading frame 2 time 80.000 -> frame 2 time 80.000 +Reading frame 2 time 80.000 -> frame 1 time 70.000 Last frame 2 time 80.000 + -> frame 2 time 80.000 +Last written: frame 2 time 80.000 -GROMACS reminds you: "C++ is tricky. You can do everything. You can even make every mistake." (Nicolai Josuttis, CppCon2017) +GROMACS reminds you: "Furious activity is no substitute for understanding." (H.H. Williams) Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output