FAQ

Content

Q: How can I check pacsmd progress ?

A. You check it by seeing pacsmd standard output or error.

INFO       2023-12-16 23:22:04  [    parser.py     -       parse      ] input_ims.toml was read successfully
INFO       2023-12-16 23:22:04  [   __main__.py    -      <module>    ] pacsmd version 0.1.1
INFO       2023-12-16 23:22:04  [   __main__.py    -        main      ] PaCS-MD starts
INFO       2023-12-16 23:22:04  [   __main__.py    -     prepare_md   ] MDsettings(..)
INFO       2023-12-16 23:22:04  [   __main__.py    -      pacs_md     ] cycle000 starts
INFO       2023-12-16 23:23:15  [superSimulator.py -  record_finished ] replica001 done
INFO       2023-12-16 23:23:18  [ superAnalyzer.py -      analyze     ] The top ranking CV is replica 1 frame 32 cv 1.864649296784787
INFO       2023-12-16 23:23:19  [     rmmol.py     -    make_top_gmx  ] topology file rmmol_top.pdb has been created in ./trial001/cycle000/replica001
INFO       2023-12-16 23:23:19  [   __main__.py    -      pacs_md     ] cycle000 done
INFO       2023-12-16 23:23:44  [     Cycle.py     -       export     ] export to cycle001 is completed
INFO       2023-12-16 23:23:46  [     rmmol.py     -     rmmol_gmx    ] trajectory file in cycle000 have been reduced
...
  • But sometimes you cannot check it because some supercomputers do not generate log files. If so, you can check it by seeing trialXXX/cycleXXX/replicaXXX/summary/progress.log. Here is a sample command for you to check quickly.
 head -n 1 trial001/cycle*/summary/cv_ranked.log | grep frame | awk '{print NR "," $6}'

And then you can get the following results. First column denotes the cycle number and second column represents CV(for example, COM distance if type == "dissociation").

1,1.864649296784787
2,1.9111852343506632
3,1.9179890510636395
4,1.9223202126596912
5,1.915256901828055
6,1.9316632729334582
7,1.9657408272709807
8,1.9565950015268871
9,1.951968749749852
10,1.9565426138983022
11,1.9765695029520212
12,2.015255318811986
13,2.047009037596073
14,2.0903023704717936
15,2.126198720722031
16,2.1582448887927432
17,2.2197207031516375
18,2.232262081387398
19,2.2752254833312677
20,2.3406157309562796
21,2.372434614483611
22,2.4393667210979166
23,2.480949213506798
24,2.575250861566694
25,2.579432883406738

Q: What should I do if there are not evaluation types that I want to use.

A: Some evaluation types are still in progress. If you need you could also develop by yourself.

  • While PaCS-MD offers many evaluation types, we could not incorporate all of them. You're welcome to utilize our template as a reference and develop your own set of evaluation types. template page.

Q: dissociation PaCS-MD takes a lot of time. Some simulations could not completed.

A: Please check COM of selected molecules.

  • Sometimes wrong selections might lead to wrong dissociation pathway and free energy.

  • But there are some examples where the selections are actually correct but not dissociated based on the initial structure.

  • You can check COM quickly by employing the following command.

$ pacs gencom traj mdtraj -s init.gro -t init.gro -ls "resid 168 || resid 253" -o com_of_r168_r253.pdb
$ pacs gencom traj mdtraj -s init.gro -t init.gro -ls "resname Lig" -o com_of_ligand.pdb
$ vmd -m init.gro com_of_r168_r253.pdb com_of_ligand.pdb

Q: Minor dissociation pathway was obtained. Is is OK ?

A: It really depends on cases but you need to check carefully by yourself.

  • Minor pathway may actually emerge, but it could stem from incorrect selections or initial structures, etc. Therefore it's crucial to assess their validity before proceeding with your simulation.

Q: I got errors during running PaCS-MD

A: Please read the error messages carefully.

  • Since PaCS-MD relies on various other libraries. many issues may arise due to incorrect settings. Before reporting your concerns to Github, please ensure whether the problem genuinely lies with PaCS-MD or not.

  • Additionally, since PaCS-MD is often employed on supercomputers, certain issues might be attributed to the supercomputers themselves. For example, PaCS-MD may encounter difficulties running on supercomputers, or errors might arise that are unrelated to the associated libraries.