[gmx-users] Protein stability using MARTINI

[Mark Abraham]

----- Original Message -----
From: Itamar Kass <itamar.kass at monash.edu>
Date: Monday, September 6, 2010 14:06
Subject: [gmx-users] Protein stability using MARTINI
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

>  HI all,
> 
> I am simulating a protein in water using the MARTINI (CG) force 
> field. My protein composed of few alpha-helices and a big tail 
> (~50AA) which is random coiled. I have built the simulation 
> system according to the procedure at 
> http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in-
> water .
> 
> After a 10ns simulation, I have visualised the system using VMD. 
> It seems like the protein had dismantled to amino acids. I see 
> groups of bids moving freely in the system.

I'm not sure what you mean here, but it seems likely that VMD's heuristics for guessing where bonds between atoms might exist aren't going to work well for a coarse-grained protein. There's probably a standard solution, for which you should Google :-)

Mark

> 
> Any idea of the problem? Any idea how to fix it?
> 
> PS I don't want to use elastic network for the random coil tail, 
> as I wish to capture as much conformation as possible.
> 
> Thanks in advance,
> Itamar.
> 
> -- 
> 
> 
> "In theory, there is no difference between theory and practice. 
> But, in practice, there is." - Jan L.A. van de Snepscheut
> 
> ===========================================
> | Itamar Kass, Ph.D.
> | Postdoctoral Research Fellow
> |
> | Department of Biochemistry and Molecular Biology
> | Building 77 Clayton Campus
> | Wellington Road
> | Monash University,
> | Victoria 3800
> | Australia
> |
> | Tel: +61 3 9902 9376
> | Fax: +61 3 9902 9500
> | E-mail: Itamar.Kass at monash.edu
> ============================================
> 
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