normal Martinizing a solvated phospholipid bilayer system

  • SinaSina92
  • SinaSina92's Avatar Topic Author
  • Offline
  • Fresh Boarder
2 months 2 weeks ago #9732 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,

Please Log in or Create an account to join the conversation.

2 months 2 weeks ago #9733 by bart
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)



Please Log in or Create an account to join the conversation.

Time to create page: 0.096 seconds