From: Jeffrey Potoff (jpotoff_at_chem1.eng.wayne.edu)
Date: Thu Aug 18 2011 - 09:22:36 CDT
In general, no. If you raise the temperature above the normal boiling
point predicted by the force field, the simulation should form a vapor
phase. I say should, because near room temperature the free energy
barrier between gas and liquid phases is quite large, so it's very
possible that a simulation run at a temperature above the normal boiling
point will stay a liquid. What you get is something metastable. This
is complicated by the fact that most of the water models, including
TIP3P, don't get the vapor pressure of water right, so as you increase
temperature, you would also have to increase pressure, but the pressure
would have to be at or above the vapor pressure predicted by the model
at that particular temperature, not the experimental value. However, if
one recognizes that most water models under-predict the vapor pressure
of water, then using the experimental value of the vapor pressure at a
particular temperature will still give you a stable liquid.
A simpler solution would be to run NVT simulations at higher temperature
after equilibrating at 1 atm and 298 K. This avoids the whole problem
of metastability. If you intend to run above 500 K, I think this is the
best way to go, unless you need to capture the effect of reduced solvent
density on protein conformation.
On 8/17/2011 2:29 PM, albus hawking wrote:
> Dear all,
> I am doing the simulation of protein undergone the temperature-jump
> condition. The protein( in this simulation, it is ubiquitin) is
> solvated in a water box and the process of raising temperature
> periodically is set. In the whole process, I keep the pressure constant.
> My question is that if I raise the temperature over the boiling
> point of water solvent, is the water box still ok? If not, could you
> please suggest me the solution?
> Thank you very much!
-- ====================================================================== Jeffrey J. Potoff jpotoff_at_chem1.eng.wayne.edu Associate Professor Wayne State University Department of Chemical Engineering and Materials Science 5050 Anthony Wayne Dr Phone:(313)577-9357 Detroit, MI 48202 Fax: (313)578-5815 http://potoff1.eng.wayne.edu ======================================================================
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