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,
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.k...@monash.edu
============================================
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