[gmx-users] Definition in martini CG force field

[mohammad agha]

Dear Gromacs users,
May I ask you to help me, Please?
1- I want to run the system with surfactant named Cocamide MEA in martini CG force field. I defined the beads as is follows:
C-C-C-C ......... C1
C-C-C ......... C2
C-C-C ......... C2
  O
  "
C-C-NH ......... P5
C-C-OH ......... P2
Are the beads correct?
2- I have problem to write the "martini_MEA.itp". I work with "martini_v2.0.itp.
I have written this file as is follows:
;;;;;; TOPOLOGIES FOR SURFACTANTS ;
; surfactants are defined here as single tail amphipatic molecules
[moleculetype]
; molname nrexcl
    MEA    1
[atoms]
; id type resnr residu atom cgnr charge
  1  C1    1    MEA  C1    1    0
  2  C2    1    MEA  C2    2    0
  3  C2    1    MEA  C3    3    0
  4  P5    1    MEA  P5    4    0
  5  P2    1    MEA  P2    5    0
[bonds]
; i j funct length force.c.
  1 2  1    0.470 1250
  2 3  1    0.470 1250
  3 4  1    0.470 1250
  4 5  1    0.470 1250
[angles]
; i j k funct angle force.c.
  1 2 3  2  180.0 25.0
  2 3 4  2  180.0 25.0
  3 4 5  2  180.0 25.0
But I think some sectins should be altered. 

May I ask you to help me, Please?


Best Regards
Sara