[gmx-users] martini coarse-grained

[dina dusti]

Hi Tsjerk,

Thank you very much from your response.
OK, it means that I should select SC4, SC4 and SC5 for tiophen (SC4s = C-C and SC5 = S)?
On the other hand, I have 2 other structure, aniline and pyrrole. If I select three beads for both of them consist of SC4, SC4 and SP1, consequently, they become similar together!!!

Please help me.

Thank you very much again.
Best Regards
Dina


________________________________
 From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: dina dusti <dinadusti at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Tuesday, April 10, 2012 11:38 PM
Subject: Re: [gmx-users] martini coarse-grained
 
Hi Dina,

Thiophen is a five-membered ring, like the histidine side-chain, which
is modeled with three beads. And then you ought to choose the bead
types such that they give good agreement with atomistic PMFs and/or
partitioning of the same compound. It's very unlikely that just
fiddling around a bit yields a suitable model.

Cheers,

Tsjerk


On Tue, Apr 10, 2012 at 8:29 PM, dina dusti <dinadusti at yahoo.com> wrote:
>
> ----- Forwarded Message -----
> From: dina dusti <dinadusti at yahoo.com>
> To: XAvier Periole <x.periole at rug.nl>
> Sent: Tuesday, April 10, 2012 10:44 PM
> Subject: martini coarse-grained
>
> Thank you very much from your response.
> I found the coordinate file of tiofen from PRODRG and I wrote .itp file for
> that according to definition of molecules in martini_v2.1_aminoacids.itp
> file.
> What is your idea about this, Please?
>
> Best Regards
> Dina
>
> ________________________________
> From: XAvier Periole <x.periole at rug.nl>
> To: dina dusti <dinadusti at yahoo.com>; Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> Sent: Tuesday, April 10, 2012 5:16 PM
> Subject: Re: [gmx-users] martini coarse-grained
>
>
> 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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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands
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