Mercurial > repos > agpetit > calculate_diameter

annotate test-data/cut_trajectories_file.log @ 7:f1dd5d99ea2d draft

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"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
author agpetit
date Mon, 30 May 2022 15:35:48 +0000
parents a7128cd8f0e1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
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c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
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1 INFO - verbose mode on
5
e504457035e5 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents: 4
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2 INFO - Start cut trajectory
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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3 INFO -
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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4 Function search_nbr_sub_traj
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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5 INFO - The input file is estimated_number_of_sub_trajectories.tsv
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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6 INFO - The length of complete trajectory is 11
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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7 INFO - The number of sub-trajectories required is 3
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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8 INFO - The elapsed time between two steps is : 10ps
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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9 INFO - The number of frames per sub-trajectory is 3
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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10 INFO - End search_nbr_sub_traj function
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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11 INFO -
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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12 Function cut_traj
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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13 INFO - The length of the trajectory is 11 frames
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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14 INFO - The elapsed time between two steps is : 10 ps
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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15 INFO - The number of sub-trajectories required is 3
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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16 INFO - .gro file is PIP2.1_test.gro
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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17 INFO - .xtc file is PIP2.1_test.xtc
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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18 INFO - Output directory is out/
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433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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19 INFO - The name of .log file is out_log/cut_trajectories.log
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c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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20 INFO - The number of cpus used is 1
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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21 INFO - Sub_trajectory 1 starts at 0 ps and ends at 20 ps
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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22 INFO - Sub_trajectory 2 starts at 30 ps and ends at 50 ps
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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23 INFO - Sub_trajectory 3 starts at 60 ps and ends at 80 ps
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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24 INFO - Launch gmx trjconv
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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25
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433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents: 2
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26 :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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27
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a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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28 Executable: /home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296/bin.AVX2_256/gmx
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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29 Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296
4
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents: 2
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30 Working dir: /tmp/tmp87fei_xs/job_working_directory/000/5/working
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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31 Command line:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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32 gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 0 -e 20 -o out/PIP2.1_test_traj_1.xtc
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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33
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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34 Will write xtc: Compressed trajectory (portable xdr format): xtc
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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35 Group 0 ( System) has 311580 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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36 Group 1 ( Protein) has 30214 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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37 Group 2 ( Protein-H) has 14908 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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38 Group 3 ( C-alpha) has 2006 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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39 Group 4 ( Backbone) has 6018 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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40 Group 5 ( MainChain) has 8016 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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41 Group 6 ( MainChain+Cb) has 9776 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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42 Group 7 ( MainChain+H) has 9926 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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43 Group 8 ( SideChain) has 20288 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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44 Group 9 ( SideChain-H) has 6892 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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45 Group 10 ( Prot-Masses) has 30214 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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46 Group 11 ( non-Protein) has 281366 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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47 Group 12 ( Other) has 281366 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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48 Group 13 ( POPC) has 83348 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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49 Group 14 ( POT) has 176 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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50 Group 15 ( CLA) has 232 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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51 Group 16 ( TIP3) has 197610 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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52 Select a group:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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53 Reading frame 0 time 0.000
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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54 Precision of PIP2.1_test.xtc is 0.001 (nm)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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55 Using output precision of 0.001 (nm)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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56
4
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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57 Reading frame 1 time 10.000 -> frame 0 time 0.000
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c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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58
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59 Reading frame 2 time 20.000 -> frame 1 time 10.000
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60
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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61 Last frame 2 time 20.000
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433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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62 -> frame 2 time 20.000
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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63 Last written: frame 2 time 20.000
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64
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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65
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433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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66 GROMACS reminds you: "The Microsecond is Within Reach" (P.J. Van Maaren)
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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67
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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68 Note that major changes are planned in future for trjconv, to improve usability and utility.
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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69 Select group for output
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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70 Selected 0: 'System'
4
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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71 :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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72
6
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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73 Executable: /home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296/bin.AVX2_256/gmx
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
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74 Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296
4
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
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75 Working dir: /tmp/tmp87fei_xs/job_working_directory/000/5/working
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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diff changeset
76 Command line:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
77 gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 30 -e 50 -o out/PIP2.1_test_traj_2.xtc
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
78
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
79 Will write xtc: Compressed trajectory (portable xdr format): xtc
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
80 Group 0 ( System) has 311580 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
81 Group 1 ( Protein) has 30214 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
82 Group 2 ( Protein-H) has 14908 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
83 Group 3 ( C-alpha) has 2006 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
84 Group 4 ( Backbone) has 6018 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
85 Group 5 ( MainChain) has 8016 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
86 Group 6 ( MainChain+Cb) has 9776 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
87 Group 7 ( MainChain+H) has 9926 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
88 Group 8 ( SideChain) has 20288 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
89 Group 9 ( SideChain-H) has 6892 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
90 Group 10 ( Prot-Masses) has 30214 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
91 Group 11 ( non-Protein) has 281366 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
92 Group 12 ( Other) has 281366 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
93 Group 13 ( POPC) has 83348 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
94 Group 14 ( POT) has 176 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
95 Group 15 ( CLA) has 232 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
96 Group 16 ( TIP3) has 197610 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
97 Select a group:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
98 Reading frame 0 time 0.000
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
99 Reading frame 0 time 30.000
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
100 Precision of PIP2.1_test.xtc is 0.001 (nm)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
101 Using output precision of 0.001 (nm)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
102
4
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents: 2
diff changeset
103 Reading frame 1 time 40.000 -> frame 0 time 30.000
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
104
4
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents: 2
diff changeset
105 Reading frame 2 time 50.000 -> frame 1 time 40.000
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
106
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
107 Last frame 2 time 50.000
4
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents: 2
diff changeset
108 -> frame 2 time 50.000
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents: 2
diff changeset
109 Last written: frame 2 time 50.000
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
110
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
111
4
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents: 2
diff changeset
112 GROMACS reminds you: "I'm Not Gonna Die Here !" (Sphere)
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
113
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
114 Note that major changes are planned in future for trjconv, to improve usability and utility.
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
115 Select group for output
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
116 Selected 0: 'System'
4
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents: 2
diff changeset
117 :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
118
6
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents: 5
diff changeset
119 Executable: /home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296/bin.AVX2_256/gmx
a7128cd8f0e1 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
agpetit
parents: 5
diff changeset
120 Data prefix: /home/aepetit/miniconda3/envs/mulled-v1-2880a0cc8fea113b095b7fdfec6d72552feed785405b8640b3b3dfce7df9d296
4
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents: 2
diff changeset
121 Working dir: /tmp/tmp87fei_xs/job_working_directory/000/5/working
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
122 Command line:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
123 gmx trjconv -f PIP2.1_test.xtc -s PIP2.1_test.gro -b 60 -e 80 -o out/PIP2.1_test_traj_3.xtc
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
124
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
125 Will write xtc: Compressed trajectory (portable xdr format): xtc
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
126 Group 0 ( System) has 311580 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
127 Group 1 ( Protein) has 30214 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
128 Group 2 ( Protein-H) has 14908 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
129 Group 3 ( C-alpha) has 2006 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
130 Group 4 ( Backbone) has 6018 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
131 Group 5 ( MainChain) has 8016 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
132 Group 6 ( MainChain+Cb) has 9776 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
133 Group 7 ( MainChain+H) has 9926 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
134 Group 8 ( SideChain) has 20288 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
135 Group 9 ( SideChain-H) has 6892 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
136 Group 10 ( Prot-Masses) has 30214 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
137 Group 11 ( non-Protein) has 281366 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
138 Group 12 ( Other) has 281366 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
139 Group 13 ( POPC) has 83348 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
140 Group 14 ( POT) has 176 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
141 Group 15 ( CLA) has 232 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
142 Group 16 ( TIP3) has 197610 elements
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
143 Select a group:
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
144 Reading frame 0 time 0.000
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
145 Reading frame 0 time 60.000
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
146 Precision of PIP2.1_test.xtc is 0.001 (nm)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
147 Using output precision of 0.001 (nm)
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
148
4
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents: 2
diff changeset
149 Reading frame 1 time 70.000 -> frame 0 time 60.000
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
150
4
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents: 2
diff changeset
151 Reading frame 2 time 80.000 -> frame 1 time 70.000
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
152
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents:
diff changeset
153 Last frame 2 time 80.000
4
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents: 2
diff changeset
154 -> frame 2 time 80.000
433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
agpetit
parents: 2
diff changeset
155 Last written: frame 2 time 80.000
2
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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433dba16af7d "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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158 GROMACS reminds you: "Furious activity is no substitute for understanding." (H.H. Williams)
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c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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159
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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160 Note that major changes are planned in future for trjconv, to improve usability and utility.
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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161 Select group for output
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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162 Selected 0: 'System'
c574ada16e76 "planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit 48a10de1b21f94ab8019d9d0e4a43e0bd9d0c31e-dirty"
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163 INFO - End cut_traj function