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

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Jun 21 2005 - 10:08:32 CDT

Hello

I didn't say it wasn't risky and I have as yet to publish my work.
However, my current research suggests that it might be possible.

The Daggett group has on several occasions asked the Schulten group to
implement the F3C water model in the NAMD/CHARMM FF.

My naive question would be, how are people using TIP4P and TIP5P if the
charm22 or charm27 parameters are tuned to TIP3P?

Regards
Brian

On Tue, 21 Jun 2005, Aaron Oakley wrote:

> Wasn't CHARMM22 parameterized specifically with TIP3P?
> I thought it was risky to use a different water model with
> CHARMM.
>
> On 20/06/2005, at 3:58 AM, 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
> >
> >
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************************************************
  Brian Bennion, Ph.D.
  Bioscience Directorate
  Lawrence Livermore National Laboratory
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