Biomolecular simulation

[Andrew Dalke]

Pornthep Sompornpisut wrote:
>         One of my interesting properties is "Solvent Accessible Surface
> Area" (SASA). The results show that SASA of the simulated structure at
> 310.5K is lower than that of the 300K. Is it strange result that the
> protein structure in aqueous solution at higher temperature has the
> lower SASA than that of the lower temperature?

The first questions I have are:
  1) what's the variability in the surface area for a given
temperature compared to the difference in area between the two.  I
would be surprised if they weren't comperable.

  2) did you keep the system at the same pressure when you increased
the temperature or was it left at a constant volume.  If the latter,
then is the compressibility of the protein enough to explain the
difference?  (Higher pressure => smaller volume => less surface area.)


						Andrew
						dalke at acm.org