- Posts: 10
The choice of bead types
- 若水无风
-
Topic Author
- Offline
- Fresh Boarder
Less
More
2 years 8 months ago #9099
by 若水无风
The choice of bead types was created by 若水无风
Hi,
i am working on the parameterization of polymer P2VP and have completed the all-atom molecular dynamics simulation, also created the CG topol. When i try to optimize the CG bonded parameter, there is an angle that It seems impossible to adjust the equilibrium angle and force constant to make its average value and distribution curve close to the reference value.
If i should change the beads at each end of the angle or modify the σ and ε between the beads? I choose the bead types based on the examples of different beads which given by the Table 3 in paper 'The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations'.
Here is the picture of beads i choose and the diagram of the angle. Mapping
Thanks for your reply.
i am working on the parameterization of polymer P2VP and have completed the all-atom molecular dynamics simulation, also created the CG topol. When i try to optimize the CG bonded parameter, there is an angle that It seems impossible to adjust the equilibrium angle and force constant to make its average value and distribution curve close to the reference value.
If i should change the beads at each end of the angle or modify the σ and ε between the beads? I choose the bead types based on the examples of different beads which given by the Table 3 in paper 'The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations'.
Here is the picture of beads i choose and the diagram of the angle. Mapping
Thanks for your reply.
Please Log in or Create an account to join the conversation.
- riccardo
-
- Offline
- Platinum Boarder
2 years 7 months ago #9134
by riccardo
Replied by riccardo on topic The choice of bead types
If you can't fit an angle it might be that your encountering steric hindrance between the beads.
It is not recommended to change epsilon/sigma because you will then modify the balance of the Martini force fields in possibly unpredictable ways.
A change of mapping might help. How big is the discrepancy between AA and CG?
It is not recommended to change epsilon/sigma because you will then modify the balance of the Martini force fields in possibly unpredictable ways.
A change of mapping might help. How big is the discrepancy between AA and CG?
Please Log in or Create an account to join the conversation.
- 若水无风
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 10
2 years 7 months ago #9140
by 若水无风
Replied by 若水无风 on topic The choice of bead types
The angle in AA model is about 60° , which in CG model is 90°.
Please Log in or Create an account to join the conversation.
Time to create page: 0.084 seconds