[gmx-users] Simulation of villin headpiece (J. Phys. Chem. B, van der Spoel and Lindahl. 107:11178)
leehk at umich.edu
Wed Aug 3 06:49:16 CEST 2005
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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