Mercurial > repos > agpetit > calculate_diameter

comparison test-data/cut_trajectories_no_file.log @ 4:433dba16af7d draft

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"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
comparison
equal deleted inserted replaced
3:b120a98cf623 4:433dba16af7d
12 INFO - The elapsed time between two steps is : 10 ps 12 INFO - The elapsed time between two steps is : 10 ps
13 INFO - The number of sub-trajectories required is 3 13 INFO - The number of sub-trajectories required is 3
14 INFO - .gro file is PIP2.1_test.gro 14 INFO - .gro file is PIP2.1_test.gro
15 INFO - .xtc file is PIP2.1_test.xtc 15 INFO - .xtc file is PIP2.1_test.xtc
16 INFO - Output directory is out/ 16 INFO - Output directory is out/
17 INFO - The name of .log file is log/cut_trajectories.log 17 INFO - The name of .log file is out_log/cut_trajectories.log
18 INFO - The number of cpus used is 1 18 INFO - The number of cpus used is 1
19 INFO - Sub_trajectory 1 starts at 0 ps and ends at 20 ps 19 INFO - Sub_trajectory 1 starts at 0 ps and ends at 20 ps
20 INFO - Sub_trajectory 2 starts at 30 ps and ends at 50 ps 20 INFO - Sub_trajectory 2 starts at 30 ps and ends at 50 ps
21 INFO - Sub_trajectory 3 starts at 60 ps and ends at 80 ps 21 INFO - Sub_trajectory 3 starts at 60 ps and ends at 80 ps
22 INFO - Launch gmx trjconv 22 INFO - Launch gmx trjconv
23 23
24 :-) GROMACS - gmx trjconv, 2020.1-Ubuntu-2020.1-1 (-: 24 :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:
25 25
26 GROMACS is written by: 26 Executable: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1/bin.AVX2_256/gmx
27 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen 27 Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1
28 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd 28 Working dir: /tmp/tmp87fei_xs/job_working_directory/000/7/working
29 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
30 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
31 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
32 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
33 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
34 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
35 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
36 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
37 Christian Wennberg Maarten Wolf Artem Zhmurov
38 and the project leaders:
39 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
40
41 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
42 Copyright (c) 2001-2019, The GROMACS development team at
43 Uppsala University, Stockholm University and
44 the Royal Institute of Technology, Sweden.
45 check out http://www.gromacs.org for more information.
46
47 GROMACS is free software; you can redistribute it and/or modify it
48 under the terms of the GNU Lesser General Public License
49 as published by the Free Software Foundation; either version 2.1
50 of the License, or (at your option) any later version.
51
52 GROMACS: gmx trjconv, version 2020.1-Ubuntu-2020.1-1
53 Executable: /usr/bin/gmx
54 Data prefix: /usr
55 Working dir: /home/aepetit/Documents/scripts/Stage-M2/wrapper/test-data
56 Command line: 29 Command line:
57 gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 0 -e 20 -o out/PIP2.1_test_traj_1.xtc 30 gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 0 -e 20 -o out/PIP2.1_test_traj_1.xtc
58 31
59 Will write xtc: Compressed trajectory (portable xdr format): xtc 32 Will write xtc: Compressed trajectory (portable xdr format): xtc
60 Group 0 ( System) has 311580 elements 33 Group 0 ( System) has 311580 elements
76 Group 16 ( TIP3) has 197610 elements 49 Group 16 ( TIP3) has 197610 elements
77 Select a group: 50 Select a group:
78 Reading frame 0 time 0.000 51 Reading frame 0 time 0.000
79 Precision of PIP2.1_test.xtc is 0.001 (nm) 52 Precision of PIP2.1_test.xtc is 0.001 (nm)
80 Using output precision of 0.001 (nm) 53 Using output precision of 0.001 (nm)
81 -> frame 0 time 0.000
82 54
83 Reading frame 1 time 10.000 -> frame 1 time 10.000 55 Reading frame 1 time 10.000 -> frame 0 time 0.000
84 56
85 Reading frame 2 time 20.000 -> frame 2 time 20.000 57 Reading frame 2 time 20.000 -> frame 1 time 10.000
86 58
87 Last frame 2 time 20.000 59 Last frame 2 time 20.000
60 -> frame 2 time 20.000
61 Last written: frame 2 time 20.000
88 62
89 63
90 GROMACS reminds you: "Your Proposal is Accepted" (Men In Black) 64 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)
91 65
92 Note that major changes are planned in future for trjconv, to improve usability and utility. 66 Note that major changes are planned in future for trjconv, to improve usability and utility.
93 Select group for output 67 Select group for output
94 Selected 0: 'System' 68 Selected 0: 'System'
95 :-) GROMACS - gmx trjconv, 2020.1-Ubuntu-2020.1-1 (-: 69 :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:
96 70
97 GROMACS is written by: 71 Executable: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1/bin.AVX2_256/gmx
98 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen 72 Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1
99 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd 73 Working dir: /tmp/tmp87fei_xs/job_working_directory/000/7/working
100 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
101 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
102 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
103 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
104 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
105 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
106 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
107 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
108 Christian Wennberg Maarten Wolf Artem Zhmurov
109 and the project leaders:
110 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
111
112 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
113 Copyright (c) 2001-2019, The GROMACS development team at
114 Uppsala University, Stockholm University and
115 the Royal Institute of Technology, Sweden.
116 check out http://www.gromacs.org for more information.
117
118 GROMACS is free software; you can redistribute it and/or modify it
119 under the terms of the GNU Lesser General Public License
120 as published by the Free Software Foundation; either version 2.1
121 of the License, or (at your option) any later version.
122
123 GROMACS: gmx trjconv, version 2020.1-Ubuntu-2020.1-1
124 Executable: /usr/bin/gmx
125 Data prefix: /usr
126 Working dir: /home/aepetit/Documents/scripts/Stage-M2/wrapper/test-data
127 Command line: 74 Command line:
128 gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 30 -e 50 -o out/PIP2.1_test_traj_2.xtc 75 gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 30 -e 50 -o out/PIP2.1_test_traj_2.xtc
129 76
130 Will write xtc: Compressed trajectory (portable xdr format): xtc 77 Will write xtc: Compressed trajectory (portable xdr format): xtc
131 Group 0 ( System) has 311580 elements 78 Group 0 ( System) has 311580 elements
148 Select a group: 95 Select a group:
149 Reading frame 0 time 0.000 96 Reading frame 0 time 0.000
150 Reading frame 0 time 30.000 97 Reading frame 0 time 30.000
151 Precision of PIP2.1_test.xtc is 0.001 (nm) 98 Precision of PIP2.1_test.xtc is 0.001 (nm)
152 Using output precision of 0.001 (nm) 99 Using output precision of 0.001 (nm)
153 -> frame 0 time 30.000
154 100
155 Reading frame 1 time 40.000 -> frame 1 time 40.000 101 Reading frame 1 time 40.000 -> frame 0 time 30.000
156 102
157 Reading frame 2 time 50.000 -> frame 2 time 50.000 103 Reading frame 2 time 50.000 -> frame 1 time 40.000
158 104
159 Last frame 2 time 50.000 105 Last frame 2 time 50.000
106 -> frame 2 time 50.000
107 Last written: frame 2 time 50.000
160 108
161 109
162 GROMACS reminds you: "That Was Really Cool" (Butthead) 110 GROMACS reminds you: "Here's the Way It Might End" (G. Michael)
163 111
164 Note that major changes are planned in future for trjconv, to improve usability and utility. 112 Note that major changes are planned in future for trjconv, to improve usability and utility.
165 Select group for output 113 Select group for output
166 Selected 0: 'System' 114 Selected 0: 'System'
167 :-) GROMACS - gmx trjconv, 2020.1-Ubuntu-2020.1-1 (-: 115 :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:
168 116
169 GROMACS is written by: 117 Executable: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1/bin.AVX2_256/gmx
170 Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen 118 Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-0569c04ab612909a373223b7f7da6469041d31d933b93b55db5a38a76d747ad1
171 Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd 119 Working dir: /tmp/tmp87fei_xs/job_working_directory/000/7/working
172 Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
173 Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
174 Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
175 Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
176 Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
177 Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
178 Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
179 Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
180 Christian Wennberg Maarten Wolf Artem Zhmurov
181 and the project leaders:
182 Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
183
184 Copyright (c) 1991-2000, University of Groningen, The Netherlands.
185 Copyright (c) 2001-2019, The GROMACS development team at
186 Uppsala University, Stockholm University and
187 the Royal Institute of Technology, Sweden.
188 check out http://www.gromacs.org for more information.
189
190 GROMACS is free software; you can redistribute it and/or modify it
191 under the terms of the GNU Lesser General Public License
192 as published by the Free Software Foundation; either version 2.1
193 of the License, or (at your option) any later version.
194
195 GROMACS: gmx trjconv, version 2020.1-Ubuntu-2020.1-1
196 Executable: /usr/bin/gmx
197 Data prefix: /usr
198 Working dir: /home/aepetit/Documents/scripts/Stage-M2/wrapper/test-data
199 Command line: 120 Command line:
200 gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 60 -e 80 -o out/PIP2.1_test_traj_3.xtc 121 gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 60 -e 80 -o out/PIP2.1_test_traj_3.xtc
201 122
202 Will write xtc: Compressed trajectory (portable xdr format): xtc 123 Will write xtc: Compressed trajectory (portable xdr format): xtc
203 Group 0 ( System) has 311580 elements 124 Group 0 ( System) has 311580 elements
220 Select a group: 141 Select a group:
221 Reading frame 0 time 0.000 142 Reading frame 0 time 0.000
222 Reading frame 0 time 60.000 143 Reading frame 0 time 60.000
223 Precision of PIP2.1_test.xtc is 0.001 (nm) 144 Precision of PIP2.1_test.xtc is 0.001 (nm)
224 Using output precision of 0.001 (nm) 145 Using output precision of 0.001 (nm)
225 -> frame 0 time 60.000
226 146
227 Reading frame 1 time 70.000 -> frame 1 time 70.000 147 Reading frame 1 time 70.000 -> frame 0 time 60.000
228 148
229 Reading frame 2 time 80.000 -> frame 2 time 80.000 149 Reading frame 2 time 80.000 -> frame 1 time 70.000
230 150
231 Last frame 2 time 80.000 151 Last frame 2 time 80.000
152 -> frame 2 time 80.000
153 Last written: frame 2 time 80.000
232 154
233 155
234 GROMACS reminds you: "Everything He Lacks, He Makes Up In Denial" (Offspring) 156 GROMACS reminds you: "Whatever Happened to Pong ?" (F. Black)
235 157
236 Note that major changes are planned in future for trjconv, to improve usability and utility. 158 Note that major changes are planned in future for trjconv, to improve usability and utility.
237 Select group for output 159 Select group for output
238 Selected 0: 'System' 160 Selected 0: 'System'
239 INFO - End cut_traj function 161 INFO - End cut_traj function