Mercurial > repos > agpetit > calculate_diameter

view test-data/cut_trajectories_file.log @ 5:e504457035e5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/mesocentre-clermont-auvergne/aubi_piaf commit b6488400d4478d46697019485e912c38ea2202a5-dirty"
author agpetit
date Mon, 30 May 2022 14:21:51 +0000
parents 433dba16af7d
children a7128cd8f0e1
line wrap: on
line source

INFO - verbose mode on
INFO - Start cut trajectory
INFO - 
Function search_nbr_sub_traj
INFO - The input file is estimated_number_of_sub_trajectories.tsv
INFO - The length of complete trajectory is 11
INFO - The number of sub-trajectories required is  3
INFO - The elapsed time between two steps is : 10ps
INFO - The number of frames per sub-trajectory is 3
INFO - End search_nbr_sub_traj function
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/000/5/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

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: "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, 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/000/5/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

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: "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, 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/000/5/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

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