Dear Amber Users,
Thank you for the explanation. I performed a constant pressure run and got
a linear relationship between volume and pressure.
Can you tell me what units the PRESSURE is output to my mdout file.
NSTEP = 5000 TIME(PS) = 1610.000 TEMP(K) = 297.21 PRESS =
-65.1
Etot = 7183.1527 EKtot = 3640.2575 EPtot =
3542.8952
BOND = 819.1416 ANGLE = 2439.9922 DIHED =
1018.7814
1-4 NB = 610.4139 1-4 EEL = -34.2619 VDWAALS =
-1837.0500
EELEC = 525.8780 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.4607 VIRIAL = 459.7223 VOLUME =
326783.6457
Density =
0.4016
Ewald error estimate: 0.6275E-04
In my input file I have set pres0=1
Thanks
Kirtana
On Sun, Jul 28, 2013 at 9:02 PM, Jason Swails <jason.swails.gmail.com>wrote:
> 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 Fri Aug 02 2013 - 16:00:03 PDT
