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view 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
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INFO - verbose mode on
INFO - Cut trajectory mode
INFO - 
Function search_nbr_steps_time_step
INFO - The input file is PIP2.1_test_check.txt
INFO - The length of the trajectory is 11
INFO - The elapsed time between two steps is : 10 ps
INFO - End search_nbr_steps_time_step functions
INFO - 
Function cut_traj
INFO - The length of the trajectory is 11 frames
INFO - The elapsed time between two steps is : 10 ps
INFO - The number of sub-trajectories required is  3
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 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, 2022.1-conda_forge (-:

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

Will write xtc: Compressed trajectory (portable xdr format): xtc
Group     0 (         System) has 311580 elements
Group     1 (        Protein) has 30214 elements
Group     2 (      Protein-H) has 14908 elements
Group     3 (        C-alpha) has  2006 elements
Group     4 (       Backbone) has  6018 elements
Group     5 (      MainChain) has  8016 elements
Group     6 (   MainChain+Cb) has  9776 elements
Group     7 (    MainChain+H) has  9926 elements
Group     8 (      SideChain) has 20288 elements
Group     9 (    SideChain-H) has  6892 elements
Group    10 (    Prot-Masses) has 30214 elements
Group    11 (    non-Protein) has 281366 elements
Group    12 (          Other) has 281366 elements
Group    13 (           POPC) has 83348 elements
Group    14 (            POT) has   176 elements
Group    15 (            CLA) has   232 elements
Group    16 (           TIP3) has 197610 elements
Select a group: 
Reading frame       0 time    0.000   
Precision of PIP2.1_test.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)

Reading frame       1 time   10.000    ->  frame      0 time    0.000      

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: "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, 2022.1-conda_forge (-:

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

Will write xtc: Compressed trajectory (portable xdr format): xtc
Group     0 (         System) has 311580 elements
Group     1 (        Protein) has 30214 elements
Group     2 (      Protein-H) has 14908 elements
Group     3 (        C-alpha) has  2006 elements
Group     4 (       Backbone) has  6018 elements
Group     5 (      MainChain) has  8016 elements
Group     6 (   MainChain+Cb) has  9776 elements
Group     7 (    MainChain+H) has  9926 elements
Group     8 (      SideChain) has 20288 elements
Group     9 (    SideChain-H) has  6892 elements
Group    10 (    Prot-Masses) has 30214 elements
Group    11 (    non-Protein) has 281366 elements
Group    12 (          Other) has 281366 elements
Group    13 (           POPC) has 83348 elements
Group    14 (            POT) has   176 elements
Group    15 (            CLA) has   232 elements
Group    16 (           TIP3) has 197610 elements
Select a group: 
Reading frame       0 time    0.000   
Reading frame       0 time   30.000   
Precision of PIP2.1_test.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)

Reading frame       1 time   40.000    ->  frame      0 time   30.000      

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: "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, 2022.1-conda_forge (-:

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

Will write xtc: Compressed trajectory (portable xdr format): xtc
Group     0 (         System) has 311580 elements
Group     1 (        Protein) has 30214 elements
Group     2 (      Protein-H) has 14908 elements
Group     3 (        C-alpha) has  2006 elements
Group     4 (       Backbone) has  6018 elements
Group     5 (      MainChain) has  8016 elements
Group     6 (   MainChain+Cb) has  9776 elements
Group     7 (    MainChain+H) has  9926 elements
Group     8 (      SideChain) has 20288 elements
Group     9 (    SideChain-H) has  6892 elements
Group    10 (    Prot-Masses) has 30214 elements
Group    11 (    non-Protein) has 281366 elements
Group    12 (          Other) has 281366 elements
Group    13 (           POPC) has 83348 elements
Group    14 (            POT) has   176 elements
Group    15 (            CLA) has   232 elements
Group    16 (           TIP3) has 197610 elements
Select a group: 
Reading frame       0 time    0.000   
Reading frame       0 time   60.000   
Precision of PIP2.1_test.xtc is 0.001 (nm)
Using output precision of 0.001 (nm)

Reading frame       1 time   70.000    ->  frame      0 time   60.000      

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: "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
Selected 0: 'System'
INFO - End cut_traj function