From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Sun Mar 29 2015 - 16:54:09 CDT
I just want to point out that the instantaneous pressure is usually
difficult to interpret because of the huge fluctuations. Don't be
surprised if you see pressures of 100 times atmospheric pressure or
negative values of similar magnitude. From statistical mechanics, you
can show that the pressure is given by sqrt(kT/(beta*V)), where beta
is the isentropic compressibility. Liquid water has a very small
compressibility (compared with gases) and the volumes that we work
with are also small. Quoting the GROMACS documentation:
"Instantaneous pressure is meaningless, and not well-defined. Over a
picosecond time scale it usually will not be a good indicator of the
true pressure....For a box of 216 waters, fluctuations of 500-600 bar
are standard. Since the fluctuations go down with the square root of
the number of particles, a system of 21600 water molecules (100 times
larger) will still have pressure fluctuations of 50-60 bar."
Jeffrey Comer, PhD
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
On Sun, Mar 29, 2015 at 3:30 PM, Brian Radak
> I don't believe NAMD uses the pressure/virial for anything during a
> conventional NVT run.
> However, in principle, it would be important to have physically sensible
> values for your system. For example, if you had an aqueous system very far
> from 1 g/mL density, this would likely be apparent as a very large external
> pressure. Put another way, ensemble equivalence between NVT and NpT can most
> easily be argued when the NVT density is near the NpT average.
> My experience is primarily with biological systems, so this may or may not
> be relevant for your system.
> On 03/29/2015 02:23 PM, Hasan haska wrote:
> Dear All,
> Is it important to see the evolution of pressure (PRESSAVG) when checking
> the equilibrium of system in NVT ensemble ? Should I consider pressure in
> NVT ?
> Brian Radak
> Postdoctoral Scholar
> Gordon Center for Integrative Science, W323A
> Department of Biochemistry & Molecular Biology
> University of Chicago
> 929 E. 57th St.
> Chicago, IL 60637-1454
> Tel: 773/834-2812
> email: radak_at_uchicago.edu
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:21:02 CST