[gmx-users] box volume and solvant density

[Justin A. Lemkul]

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.

-Justin

> Thanks in advance for your insights
> JP Grivet
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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