[gmx-users] Re: box volume and solvant density
dommert at icp.uni-stuttgart.de
Mon May 31 17:43:29 CEST 2010
On 31.05.2010, at 17:37, grivet wrote:
> 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 ?
No this is because you are simulating NVT, so you know your box dimensions.
>> 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 ?
>>>> 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
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Institute for Computational Physics
EMail: dommert at icp.uni-stuttgart.de
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