On Sun, Jul 28, 2013 at 4:29 PM, kirtana S <skirtana4.gmail.com> wrote:
> Dear Amber Users,
>
> How can I determine isothermal compressibility from my NPT simulations.
>
Googling "isothermal compressibility", I got this website as the third hit:
http://alcheme.tamu.edu/?page_id=755.
I believe that the standard way of computing isothermal compressibilities
is by using the volume fluctuations (the second equation in the website I
gave you), where the numerator is the variance.
The bad news is that Amber 12 and earlier supports only the Berendsen
barostat, which is known to suppress fluctuations compared to a method that
samples rigorously from the NPT ensemble, so I doubt that you can use such
simulations to reliably calculate isothermal compressibilities.
I know there has been some effort put into implementing a Monte Carlo
barostat in sander and pmemd which is a rigorous barostat, but that will
not be available until (hopefully) Amber 14 next year.
I've heard that setting the barostat coupling constant (taup) to a small
value (~0.5 to 1) gives 'correct' fluctuations, so that may be something
worth looking into as well...
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Jul 28 2013 - 21:30:02 PDT
