[gmx-users] Simulation of villin headpiece (J. Phys. Chem. B, van der Spoel and Lindahl. 107:11178)

Hwankyu Lee leehk at umich.edu
Wed Aug 3 06:49:16 CEST 2005

Dear Gromacs-users,

I read the paper   "Brute-force molecular dynamics simulations of 
villin headpiece: Comparison with NMR parameters"  van der Spoel and 
Lindahl. J. Phys. Chem. B, 107, 11178., and then tried to simulate 
villin headpiece to see if I can get stable alpha-helical structure of 
the protein, similar to the results in that paper.
So, I applied exactly same conditions (OPLS-AA with TIP4P water, 
protein PDB:1VII, 300K, ~70 mM NaCl, NPT, gromacs v3.1.4, adding dummy 
atoms (because the paper says that it doesn't make difference)), but 
couldn't get stable alpha-helixes (figure 8 in that paper). In that 
paper (fig 8), stable alpha-helixes are consistently shown in whole 
simulation time.    But, when I tried this, helixes became turn or coil 
over 10ns and couldn't see alpha-helixes at all.  I also tried 
different conc. of NaCl, but didn't work.
I cannot understand why I fail to have same results from same 
simulations.    Did I miss something important in this simulation?
If I can hear any advice from Dr. van der Spoel, Dr. Lindahl, or any 
person who tried this, I would really appreciate it.


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