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Martinizing a solvated phospholipid bilayer system
- SinaSina92
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1 month 3 weeks ago #9732
by SinaSina92
Martinizing a solvated phospholipid bilayer system was created by SinaSina92
Hi everyone,
I'm trying to Martinize a solvated phospholipid bilayer box (including ions such as Na and Cl). I have seen the Martinize tutorials in which we can build a CG system and solvate it with CG beads but my intention is to convert all of the AA system to CG.
I have tried Martinize and Vermouth but there is always a problem with converting water molecules (in addition to all the problems/errors related to lipid conversion). I know that grouping of the water molecules and converting them to CG beads is one of the major problems but just wanted to know if there is any code/algorithms that has been already used for this purpose?
Also, considering the available tools, I would appreciate it if anyone can suggest me which Martini version (2 or 3?) is more suitable for this work?
Thanks in advance,
Sina
I'm trying to Martinize a solvated phospholipid bilayer box (including ions such as Na and Cl). I have seen the Martinize tutorials in which we can build a CG system and solvate it with CG beads but my intention is to convert all of the AA system to CG.
I have tried Martinize and Vermouth but there is always a problem with converting water molecules (in addition to all the problems/errors related to lipid conversion). I know that grouping of the water molecules and converting them to CG beads is one of the major problems but just wanted to know if there is any code/algorithms that has been already used for this purpose?
Also, considering the available tools, I would appreciate it if anyone can suggest me which Martini version (2 or 3?) is more suitable for this work?
Thanks in advance,
Sina
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- bart
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1 month 3 weeks ago #9733
by bart
Replied by bart on topic Martinizing a solvated phospholipid bilayer system
Hoi Sina,
I know there were some algorithm published to do the water conversion a while ago using graph logic (i cannot find it anymore), however, so far I have not yet encountered enyone who has a workflow in which they take a AA box as a whole and convert it to CG. It is also and outstanding dream for me, but as of yet I do not think this is an approach widely used.
Instead people map te proteins and lipids using martinize2. Water is then added using GROMACS solvate, Insane or TS2CG. I usually use insane. Specific placement of ions could be kept as ions are also a single bead in Martini. (Remeber a CG water bead is 4 AA waters and a CG ion bead is 3-4 waters and an ion).
I would use Martini3 for your problem, although Martini2 probably works good as well. (I like staying up to date)
Cheers,
Bart
I know there were some algorithm published to do the water conversion a while ago using graph logic (i cannot find it anymore), however, so far I have not yet encountered enyone who has a workflow in which they take a AA box as a whole and convert it to CG. It is also and outstanding dream for me, but as of yet I do not think this is an approach widely used.
Instead people map te proteins and lipids using martinize2. Water is then added using GROMACS solvate, Insane or TS2CG. I usually use insane. Specific placement of ions could be kept as ions are also a single bead in Martini. (Remeber a CG water bead is 4 AA waters and a CG ion bead is 3-4 waters and an ion).
I would use Martini3 for your problem, although Martini2 probably works good as well. (I like staying up to date)
Cheers,
Bart
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