Re: Solvent model other than TIP3 for use with CHARMM FF in NAMD??

From: Brian Bennion (
Date: Mon Jun 20 2005 - 10:26:49 CDT


I am in the process of traveling this road. Since I did come from the
virtually only laboratory that uses encad and f3c, I have been playing
with F3C in namd. I still need to do a lot more analsysis but it seems to
work out well.


On Sun, 19 Jun 2005, Leonardo Sepulveda Durán wrote:

> 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

  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
  P.O. Box 808, L-448
  7000 East Avenue phone: (925) 422-5722
  Livermore, CA 94550 fax: (925) 424-6605

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