Mercurial > repos > agpetit > calculate_diameter
diff test-data/cut_trajectories_no_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_no_file.log Fri May 27 07:36:52 2022 +0000 +++ b/test-data/cut_trajectories_no_file.log Fri May 27 09:07:29 2022 +0000 @@ -14,45 +14,18 @@ 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/000/7/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 @@ -78,52 +51,26 @@ 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: "Your Proposal is Accepted" (Men In Black) +GROMACS reminds you: "It is now quite lawful for a Catholic woman to avoid pregnancy by a resort to mathematics, though she is still forbidden to resort to physics and chemistry." (Henry Louis Mencken) 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/000/7/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 @@ -150,52 +97,26 @@ 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: "That Was Really Cool" (Butthead) +GROMACS reminds you: "Here's the Way It Might End" (G. Michael) 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/000/7/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 @@ -222,16 +143,17 @@ 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: "Everything He Lacks, He Makes Up In Denial" (Offspring) +GROMACS reminds you: "Whatever Happened to Pong ?" (F. Black) Note that major changes are planned in future for trjconv, to improve usability and utility. Select group for output