[gmx-users] box volume and solvant density

Justin A. Lemkul jalemkul at vt.edu
Mon May 31 16:29:24 CEST 2010

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.

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.


>> 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


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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