[gmx-users] Protein stability using MARTINI
itamar.kass at monash.edu
Mon Sep 6 05:32:42 CEST 2010
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
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
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at monash.edu
More information about the gromacs.org_gmx-users