求助：如何对聚合物链（10个重复单元）进行限制，使经过NPT模拟后得到想要的构型？

neoje

原文献中每根（聚合物）链是4个重复单元，总共两根链，经40 ns左右的NPT模拟即会形成一种“双螺旋”构型，最终稳定构型见120ns_PBDT.gro文件

我现在每根（聚合物）链是10个重复单元，总共两根链，想通过模拟复刻这种双螺旋构型，目前的问题是，即使在mdp文件中加上“constrain=all-bonds”，经过10 ns的NPT模拟后，分子构型仍会出现如图所示的蜷曲状，

我的目标是让两根链在保持刚性的同时尽可能发生双螺旋缠绕，想请教下各位前辈，应该进行怎样的处理能够达到目标呢（这个问题已经困扰近一个星期了，恳请各位前辈指点一下！）

student0618

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.
  

neoje

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!

neoje

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!

student0618

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.

neoje

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