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

[Florian Dommert]

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.

/Flo
>> 
>> 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
>> 
>> ========================================
> 
> -- 
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--
Florian Dommert
Dipl.-Phys.

Institute for Computational Physics

University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

Phone: +49(0)711/685-6-3613
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EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert

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