student0618 发表于 2024-9-9 00:38
It's probably useful to try reproducing the exact protocol in literature first, in case of any probl ...

Anyway, thanks~ I'll follow your advice

It's probably useful to try reproducing the exact protocol in literature first, in case of any problems when trying to reproduce a similar system.

Note the difference between constraints and restraints. You probably want a kind of secondary structure or dihedral restraints from my understanding?

But anyway it's probably not a good idea to make it too rigid if you want to simulate self assembly, the polymer may need to adapt different intermediate conformations before forming the desirable helix.

Other factors to be considered include pressure coupling scheme, isotropic or anisotropic, simulation length (10 ns vs 40 in literature. You're using longer chain, likely need longer time), as previously mentioned.

It's also possible that in literature they've optimized the dihedral parameters for the polymer instead of using generalized parameters. Need to double-check, in that case.

student0618 发表于 2024-9-8 18:27
1. “constrain=all-bonds” is NOT related to your results.
2. Are you using the same forcefield as  ...

Thanks very much for replying!
1. I try this "constrain=all-bonds" to avoid chain bending, but failed (and this is the main reason I'm here to post for help)

2. In literature it uses Amber in SI and here I use GAFF (in our group currently we often use it).

3. I study the same polymer as in literature, but the number of repeating unit is different (3-4 in literature and 10 in mine, personally I believe it's the main difference), and the pressure coupling is also different. I'll try to control the same pressure coupling condition. Thanks for this advice!

Thanks very much for replying!
1. I try this "constrain=all-bonds" to avoid chain bending, but failed (and this is the main reason I'm here to post for help)

2. In literature it uses Amber in SI and here I use GAFF (in our group currently we often use it).

3. I study the same polymer as in literature, but the number of repeating unit is different (3-4 in literature and 10 in mine, personally I believe it's the main difference), and the pressure coupling is also different. I'll try to control the same pressure coupling condition. Thanks for this advice!

1. “constrain=all-bonds” is NOT related to your results.
2. Are you using the same forcefield as in literature?

3. Have you tried to use the exact protocol in literature?

• i.e. same polymer, same simulation length, same pressure coupling.
• 10ns could be just too short if they need 40.