[gmx-users] isothermal-isometric ensemble on gromacs

[Justin Lemkul]

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

-- 
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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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