[gmx-users] Definition in martini CG force field

[Peter Kroon]

Hi Sara,

first off, you're probably better off asking these Martini-specific
questions on the Martini forum (cgmartini.nl)
Secondly, some answers are inline

On 11/11/15 10:57, mohammad agha wrote:
> 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?
They seem reasonable, you may want to switch the amide and alcohol.
Ultimately, check the solvation free energy; preferably against
experimental data.
> 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. 
Why?
>
> May I ask you to help me, Please?
>
>
> Best Regards
> Sara
Peter