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Bond/angle distribution not matching for standard C1 chain
- yogi@martini
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6 years 3 months ago #7470
by yogi@martini
Bond/angle distribution not matching for standard C1 chain was created by yogi@martini
Hello experts,
I am parameterizing new lipid with hair pin structure, two tails attached to one head.
I have atomistic trajectories for lipid bilayer (simulation using gromacs with gromos FF). Now I am developing martini model. After 4-1 mapping, I kept standard bond length 0.47 and 1280 force.c, and 180 angle with 25 force.c. for tails. And assigned bond/angle for headgroup beads from atomistic simulation. I did self assembly simulation. I am getting good agreement between AA and CG for headgroup beads but not for tail atoms which are simple C1-C1-C1... tail. The bond angle distribution which I am getting can be found here - https://imgur.com/a/Yx7GY
I am parameterizing new lipid with hair pin structure, two tails attached to one head.
I have atomistic trajectories for lipid bilayer (simulation using gromacs with gromos FF). Now I am developing martini model. After 4-1 mapping, I kept standard bond length 0.47 and 1280 force.c, and 180 angle with 25 force.c. for tails. And assigned bond/angle for headgroup beads from atomistic simulation. I did self assembly simulation. I am getting good agreement between AA and CG for headgroup beads but not for tail atoms which are simple C1-C1-C1... tail. The bond angle distribution which I am getting can be found here - https://imgur.com/a/Yx7GY
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- Pim
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6 years 3 months ago #7472
by Pim
Replied by Pim on topic Bond/angle distribution not matching for standard C1 chain
Hey, quick reply:
I'd say that your CG results, although the bond length is a bit lower than expected maybe, are what is to be expected from such a simulation. I'm a bit surprised by the very narrow atomistic distributions to be honest. Atomistic simulations of hexadecane, for example, give average angles of 137 deg. according to the 2004 Martini paper (probably also not very hard to check and I'm sure there's more experts here that can comment). So it's a bit stereotypical to say, but are you sure your gromos simulations are accurate? If you want to match those you'll have to deviate from the 0.47/1250 and 180/25 distributions for this lipid.
I'd say that your CG results, although the bond length is a bit lower than expected maybe, are what is to be expected from such a simulation. I'm a bit surprised by the very narrow atomistic distributions to be honest. Atomistic simulations of hexadecane, for example, give average angles of 137 deg. according to the 2004 Martini paper (probably also not very hard to check and I'm sure there's more experts here that can comment). So it's a bit stereotypical to say, but are you sure your gromos simulations are accurate? If you want to match those you'll have to deviate from the 0.47/1250 and 180/25 distributions for this lipid.
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