[gmx-users] Martini

dina dusti dinadusti at yahoo.com
Thu Mar 8 21:24:02 CET 2012

Dear Dariush, 

Thank you very much from your response.
Then you tell me that the definition of aniline and pyrrole, is correct?
Is your mean about SC5 for tiofen means that it is defined as SC4 and SC5 for tiofen? indeed I had doubt about this definition because S is without H in tiofen.

May I know your cause for this definition, Please?

Best Regards

 From: Dariush Mohammadyani <d.mohammadyani at gmail.com>
To: dina dusti <dinadusti at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Thursday, March 8, 2012 11:24 PM
Subject: Re: [gmx-users] Martini

SC5 does not work?

Kind Regards,
Dariush Mohammadyani
Department of Structural  Biology
University of Pittsburgh School of Medicine
Biomedical Science  Tower 3
3501 Fifth Avenue
Pittsburgh, PA 15261

On Thu, Mar 8, 2012 at 2:34 PM, dina dusti <dinadusti at yahoo.com> wrote:

Dear Gromacs Specialists,
>May I ask you to help me for definition of pyrrole, tiofen and aniline in MARTINI coarse-grained force field, Please?
>I defined them as following:
>aniline (one benzene ring+NH2) = SC4, SC4, SNd
>pyrrole (one aromatic ring consists of 4 carbon and one NH) = SC4, SP1
>tiofen (one aromatic ring consists of 4 carbon and one S) = ???
>May I ask you to tell me your idea about these molecules, Please?
>Thank you in advance.
>Best RegardsDina
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