[gmx-users] CG lipid model

[ashish misra]

Hi all,

I am planning on using the coarse grained lipid model of Marrink et al (JPC-B,
108:750) to study the micelle formation behavior for the following monomer.


      C9  C9
      |   |
      C=O C=O
 (-)  |   |
  O   O   O
  |   |   |     100 units
O=C-C-C-C-C-C-O-(C-C-O)-C
    |   |   ||
    O   O   O
    |   |
    C=O C=O
    |   |
    C9  C9

C- methyl groups


I am thinking of reducing the monomer by using the following groupings.

1)
    |
    O=C - Qa
2)
    C
    |   - P
    O
    |
    C=O
3)
    C9  - C3
4)
   (C-C-O) - Na

which reduces the monomer to:

     C3  C3
     |   |    100
Qa-P-P-P-P-P-(Na)-C
   |   |
   C3  C3

and then employing the same force field as has been described.

In the model, I have trouble understanding the equilibrium bond angle for
alkanes as 180. Wouldn't a value closer to 110 be more appropriate?

I would appreciate suggestions about equilibrium angle values in the
monomer representation


Thanks
Ashish