[gmx-users] martini coarse-grained

dina dusti dinadusti at yahoo.com
Tue Apr 10 10:44:57 CEST 2012

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

; molname       nrexcl
  TIO         1

; id    type    resnr   residu  atom    cgnr    charge
  1     SC4     1         TIO     SI1     1     0 
  2     SC5     1         TIO     SI2    2     0 

; 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
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