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

From: apw397_at_soton.ac.uk
Date: Wed Jun 22 2005 - 10:41:58 CDT

Leonardo,

Just to comment- I believe that it is frequently observed from literature
that above optimised temperatures (i.e. 298/300 K), proteins in implicit
solvent are far more mobile than when modelled in explicit waters. This is
not a deficit particular to the water model, but the optimisation of the
forcefield which assumes much lower temperature to that which you are
using. Until forcefields are parameterised with a temperature component (I
believe this has been done, but is not ready for protein simulations), it
is unlikely that temperature information will be comparable to experiment
or between water models. Personally I would not consider changing to a
water model for which your protein parameters are not optimised.

I have done a range of explicit water high temperature simulations for
parallel tempering, and generally find proteins that unfold <2ns in
implicit solvent <400 K to remain stable(ish) for up to 10ns at 450K+.

The only other comment I would make is to check your internal temperature.
There is a lot of evidence to suggest poor equilibration can result in
uneven temperature distributions between solvent and solute that can affect
dynamics. You can do this by outputing velocity information and scripting a
temperature calculation to either separate solvent and solute, or slabs of
atoms throughout your cell to confirm even kinetic energy distribution. If
you are confident that your system is slowly equilibrated to the desired
temperature using, for example, the Langevin thermostat, then this step is
probably unnecessary.

Please note that if you raise your temperature much higher you may need to
check energy conservation. I have found a timestep of 1fs is required about
500K (and I use 2fs <500K).

Adrian

Quoting Leonardo Sepulveda Durán <leonardosepulveda_at_gmail.com>:

> 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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