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Tsjerk / Insane

INSert membrANE - A simple, versatile tool for building coarse-grained simulation systems
GNU General Public License v2.0
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Insane and GoMartini - Charge determination #81

Open qoraj opened 8 months ago

qoraj commented 8 months ago

Hey i am working on a GoMartini structure of my protein and i recognized that if a use my coarse-grained protein structure, which i made with martinize2, insane.py counts the virtual CA beads into the charge determination of the protein. I know that i could work around this pretty easily, but i like the fact, that i can set up my system and change the salt concentration so easily with insane.py maybe this can be adjusted quite easily? Or i am doing something wrong?

Kind regards,

Denis

Tsjerk commented 7 months ago

I don't see where in the code this would be happening. Can you try the latest version (1.2.0) and if it doesn't work send me the input and output?

aminsagar commented 1 month ago

Hi @Tsjerk . I am experiencing the same issue with the pip installable version. Did you get a chance to look at the files? Otherwise, I can provide the files to reproduce this issue.

Best, Amin.

qoraj commented 3 weeks ago

Hi @aminsagar,

I haven't done any CG simulations in a long time, but i stumbled over this publication: https://pubs.acs.org/doi/10.1021/acs.jctc.3c01222. Under associated content they have a link to a tutorial for switching Go̅ -Martini simulations. And in this tutorial they describe the same problem with a quite elegant solution. I will add the tutorial.

Here a snippet of the tutorial and the full tutorial:

wget http://www.cgmartini.nl/images/tools/insane/insane.py python2 insane.py -f Protein_Active_cg.pdb -box 8,8,10 -l POPC -o ions.gro -salt 0.15 -charge auto -center -sol W 2>system.top

Repair the wrong ion names and ion counts.

sed -i "s/NA+ NA+/NA NA/g" ions.gro sed -i "s/CL- CL-/CL CL/g" ions.gro sed -i "s/NA+/NA /g" system.top sed -i "s/CL-/CL /g" system.top vi system.top # Delete 2 CL in system.top and ions.gro. The error is becaus e the virtual atoms without charges are also calculated by insane.py. vi ions.gro

README.pdf