dayu8278 发表于 2024-7-7 11:28
你用卢老师的genmem程序建立一个DPPC的膜，这样膜的尺寸都可以自己定制，然后跑一个平衡的膜，然后再添加小 ...

好的 谢谢

sobereva 发表于 2024-7-7 16:48
推荐用genmixmem构建结构，拓扑文件和力场问题下文里也写了
生成混合组分的磷脂双层膜结构文件的工具genmi ...

好的，谢谢老师

推荐用genmixmem构建结构，拓扑文件和力场问题下文里也写了
生成混合组分的磷脂双层膜结构文件的工具genmixmem
http://sobereva.com/245

你用卢老师的genmem程序建立一个DPPC的膜，这样膜的尺寸都可以自己定制，然后跑一个平衡的膜，然后再添加小分子

student0618 发表于 2024-7-6 23:25
That paper means they built the lipid layer in CHARMM-GUI which is a tool for input preparation. Jus ...

好的，谢谢

Seyilaxa 发表于 2024-7-6 23:16
没有提到用charmm36力场，用的就是GROMOS力场
而且也没有模拟中途换力场的理由

对，文献里面是没有提到charmm力场但是自己用charmmgui建细胞膜的时候下载的压缩包里面好像是用的charmm力场（拓扑文件里面），所以有点困惑

That paper means they built the lipid layer in CHARMM-GUI which is a tool for input preparation. Just take the coordinates, like how we get protein structure from PDB.

Then they do MD with GROMOS forcefield. Although they're spelling it wrong.
From the 3rd paragraph seems to be Berger lipid which is compatible with GROMOS. Berger lipid parameters is no longer available though, due to a problem in the forcefield. Just based on your figure, I didn't read the original paper.

BTW they have quite a number of typos and weird protocol in that paper...

没有提到用charmm36力场，用的就是GROMOS力场
而且也没有模拟中途换力场的理由