[gmx-users] box volume and solvant density

Justin A. Lemkul jalemkul at vt.edu
Mon May 31 16:25:21 CEST 2010

grivet wrote:
> Dear all,
> I am running simulations of pure water at various temperatures. My first
> step is an annealing from the previous temperature to the next one,
> using a NPT ensemble. Using the result of that, I run an NVT simulation.
> Where can I recover the box average box dimensions, volume and density
> of water in the NVT run ?

Use g_energy.

> Using g_density, I am surprised to find that the density is varying by
> several percent; shouldn't it remain constant ?

Is this under NPT?  "Constant" and "fixed" are somewhat different.  "Constant" 
implies conserved, fluctuating about an average value.  "Fixed" implies that 
there is no variation, essentially an artificial condition.


> Thanks in advance for your insights
> JP Grivet


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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