[gmx-users] isothermal-isometric ensemble on gromacs

[Antonio Baptista]

Well, the terminology is an old one, but not very common. An isometric 
ensemble is generally one in which the "extension" in the mechanical work 
term is kept constant. Thus, it may mean that the volume is kept constant 
in a volume/pressure system, that the area is kept constant in a 
area/surface tension system, that the length is kept constant in a 
length/linear tension system, etc. It is perhaps more common in the last 
case. Anyway, in the paper you mentioned it is probably just an unusual 
way of saying "constant-volume", as Justin pointed.

Cheers,
Antonio


On Tue, 3 Jun 2014, Justin Lemkul wrote:

>
>
> On 6/3/14, 10:05 AM, Carlos Navarrro Retamal wrote:
>>
>> Dear gromacs users,
>> I’m trying to replicate the following paper 
> http://www.ncbi.nlm.nih.gov/pubmed/?term=Desiccation+Induced+Structural+Alterations+in+a+66-Amino+Acid+Fragment+of+an+Anhydrobiotic+Nematode+Late+Embryogenesis+Abundant+(LEA)+Protein.
>> According to the methodology, they used gromacs 3.3.3 software and they 
> performed several MD simulations using the isothermal-isometric ensemble.
>> This is the first time i’ve heard about this ensemble. Which kind of 
> properties does this ensemble considerer? An even more importantly, how can i 
> set up this ensemble in a MD simulations on gromacs?
>
> From briefly looking at the methods, it sounds like they put all of their 
> systems in boxes of the same size (hence isometric), and if those boxes were 
> invariant (as is implied), then it's a constant volume ensemble, so it's NVT 
> in 
> this case.  The language is a bit nonstandard here, but that's what I'd 
> assume 
> they used.
>
> -Justin
>
> -- 
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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