[gmx-users] Protein stability using MARTINI

Itamar Kass itamar.kass at monash.edu
Mon Sep 6 05:32:42 CEST 2010

  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.

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,


"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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