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

[Justin A. Lemkul]

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, it's probably because you're using an NVT ensemble.  See the comment from my 
previous message.  If the values can't change then they likely won't be written 
to the .edr file (since it's a waste of space).

-Justin

>> 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
>>
>> ========================================
> 

-- 
========================================

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

========================================