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unanswered Questions on insane.py

  • F.Keller
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6 years 11 months ago #7277 by F.Keller
Questions on insane.py was created by F.Keller
Dear Martini-Community,
I have a few questions on the insane.py-tool and would very much appreciate your help:
  1. Regarding the routine to add the proper number of ions to a system, which is:
    ncl  = max(max(0,charge),int(.5+.5(concentration*nsol/(27.7+concentration)+charge)))
nna  = ncl - charge
    Why considering the charges as for a negatively charged systems this would decrease the actual salt concentration? Or am I wrong with this one?
    I added a naive solution with just adding a number of salt pairs roughly creating the wanted salt concentration and then adding the proper number of counter ions, disregarding any solvation volume effects.

  2. Also the entries for the GLYCOLIPIDS definition appeared strange to me as there was a gap on position 25 for lipids DPG1 to XNG3 which I think is related to the problem stated here: Missing_PNG3_atoms
    Is this definition actually wrong? I added a suggestions for the solution in the bottom linked insane.py file.

  3. I get an error message when defining Lysophosphatidylcholine lipids with 2 linker beads stating that the number of tails must equal the number of linkers, though in the .itp definition those lipids very well have 2 linker beads. Is this a bug? I just commented this if-statement out for my purpose.
I provide my modified file here (comments with "<date>FK" mark my modifications) :
www.dropbox.com/s/dwlyh0gwryiqgcv/insane_mod.py?dl=0
Thanks in advance for your help!
Best,
Fabian

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