[gmx-users] martini coarse-grained

[XAvier Periole]

Where did you find the topology?

On Apr 10, 2012, at 10:44 AM, dina dusti wrote:

> Dear GROMACS Specialists,
>
> I have doubt about definition of tiofen ring in MARTINI CG force  
> field. May I ask you to help me, Please?
> I defined if as: SC4 and SC5, that SC5 is as S-C-C and SC4 is as C- 
> C. Is it right?
> Or should I change SC5 to C-S-C for .gro file?
> And my definition of tiofen in .itp file it is as followed , Please  
> say me that is it right?
>
> ;;;;;;  TIOFEN
>
> [moleculetype]
> ; molname       nrexcl
>   TIO         1
>
> [atoms]
> ; id    type    resnr   residu  atom    cgnr    charge
>   1     SC4     1         TIO     SI1     1     0
>   2     SC5     1         TIO     SI2    2     0
>
> [constraints]
> ; i j   funct   length
>   1 2     1     0.27
>
> Because I for benzene see a triangle in ngmx program, but for this  
> see a line. Please help me to correction of mistakes.
> Thank you very much in advance.
>
> Best Regards
> Dina
>
>
>
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