Current time: 01-16-2021, 03:32 AM Hello There, Guest! (LoginRegister)


Post Reply 
 
Thread Rating:
  • 0 Votes - 0 Average
  • 1
  • 2
  • 3
  • 4
  • 5
Coarse-Grained Parameter Files
10-07-2012, 12:45 PM
Post: #2
RE: Coarse-Grained Parameter Files
Hi Jason,

The parameters for most of the coarse-grained simulations are recorded in the corresponding papers. I haven't had a time to formalize the parameters for the pDMD package. Based on the tutorial and the parameters in the paper, you can create input files for pDMD simulations.

2-bead:
F. Ding, Dokholyan V.N., Buldyrev V.S., Stanley H.E. and Shakhnovich E.I. Direct molecular dynamics observation of protein folding transition state ensemble. Biophys J., 86 (6): December 2002

4-bead:
F. Ding, Borreguero J.M., Buldyrev S.V., Stangley H.E. and Dokholyan N.V., A mechanism for alpha-helix to beta-hairpin transition, Proteins: Structure, Function and Genetics, 53:220-228 (2003)

Pseudo-allatom:
F. Ding, S. V. Buldyrev, and N. V. Dokholyan, "Folding Trp-cage to NMR resolution native structure using a coarse-grained protein model", Biophys. J., 88: 147-155 (2005).
Find all posts by this user
Quote this message in a reply
Post Reply 


Messages In This Thread
Coarse-Grained Parameter Files - jasonlai - 09-27-2012, 08:00 AM
RE: Coarse-Grained Parameter Files - fding - 10-07-2012 12:45 PM

Forum Jump:


User(s) browsing this thread: 1 Guest(s)