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Martinize - solvated neutralized system
- simoncks1994v2
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7 years 1 month ago #7178
by simoncks1994v2
Martinize - solvated neutralized system was created by simoncks1994v2
Hi everyone,
I am a newbie to Martini. I have a system solvated and neutralized with Na / Cl ions and I want to use Martinize to CG it. I am choosing martini22. However, the script never converts H2O and ions into the new pdb.
Therefore I suppose there is a way to generate ions in CG-ed system? Currently, I am using water.gro to gmx solvate the CG-protein and manually add the topology in "system.top".
Is there any suggestion or reference I should look into?
Thanks,
Simon
I am a newbie to Martini. I have a system solvated and neutralized with Na / Cl ions and I want to use Martinize to CG it. I am choosing martini22. However, the script never converts H2O and ions into the new pdb.
Therefore I suppose there is a way to generate ions in CG-ed system? Currently, I am using water.gro to gmx solvate the CG-protein and manually add the topology in "system.top".
Is there any suggestion or reference I should look into?
Thanks,
Simon
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- tsjerk
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7 years 1 month ago #7187
by tsjerk
Replied by tsjerk on topic Martinize - solvated neutralized system
Hi Simon,
Martinize currently only coarse grains protein or nucleic acids. To add solvent and ions (and lipids, sugars and whatnot), you can use insane.
The problem coarse graining solvent/ions is the grouping of molecules, since each coarse grained water (ion) represents 4 water molecules (and an ion).
Cheers,
Tsjerk
Martinize currently only coarse grains protein or nucleic acids. To add solvent and ions (and lipids, sugars and whatnot), you can use insane.
The problem coarse graining solvent/ions is the grouping of molecules, since each coarse grained water (ion) represents 4 water molecules (and an ion).
Cheers,
Tsjerk
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