From: Leonardo Sepulveda Durán (leonardosepulveda_at_gmail.com)
Date: Sun Jun 19 2005 - 12:58:18 CDT
Hello everyone!!!
I just have finished some dynamics at 498K using explicit solvent NPT
or NVE in NAMD, to unfold a protein. Nevertheless, it maintain its
stability in my 2ns simulations. I have done implicit solvent
simulations in CHARMM at 498K and the protein easily unfolds. So I
think there would be some issue In the TIP3 solvent model (or better,
he relation beetween protein and water paremeters) wich favours native
state ensemble even under unfolding conditions used in literature (but
with other solvent model and forcefield, F3C, flexible 3 center water
model, and ENCAD), That is why I was wondering if there is another
water model compatible with CHARMM FF able to be used in NAMD, to see
if with it unfolding is easier to achieve.
I have not revised the diferences beetween F3C and TIP3 yet, but I
Think if the VdW parameters are more atractive unfolding can be
favoured, I guess it would be more important than the use of bond and
angle degrees of freedom, but I am not sure of that.
So any comment about the issue would be very helpful
Thanks
Leonardo Sepúlveda Durán
Universidad de Chile
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