[gmx-users] Re: box volume and solvant density

[grivet]

Le lundi 31 mai 2010 à 10:29 -0400, Justin A. Lemkul a écrit :
> 
> Justin A. Lemkul wrote:
> > 
> > 
> > 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.
Appaerently no; g_energy gives me a choice of 37 variables to print
(energies, pressure tensor, virial, etc..) but not box dimensions,
volume or density. Is this because I am using 4.0.5 ?
> 
> I should also add that under an NVT ensemble, none of these values will have 
> changed from whatever the initial conditions were.  Only under the influence of 
> pressure coupling does the density vary (since the box vectors fluctuate). 
> Volume is constant by virtue of the fact that you're using NVT.
> 
> -Justin
> 
> >> Using g_density, I am surprised to find that the density is varying by
> >> several percent; shouldn't it remain constant ?
> >> Thanks in advance for your insights
> >> JP Grivet
My mistake. g_density outputs *partial* densities, with a default number
of slices = 50. Setting -sl 0 recovers a single normal density. 
> > 
> 
> -- 
> ========================================
> 
> 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
> 
> ========================================