Re: [Apbs-users] single-trajectory vs three-trajectory

[Jason S. <jas...@gm...>]

Hello,

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032

On Jun 25, 2011, at 12:01 PM, "Baker, Nathan" <Nat...@pn...> wrote:

> Hi Dimitrios –
> 
>  
> 
> I think the assumption that the internal energy cancels out the entropy is a weak argument and I strongly doubt it’s been rigorously demonstrated anywhere.
> 
>  
> 
> __________________________________________________ 
> Nathan Baker 
> Pacific Northwest National Laboratory
> Tel:  509-375-3997
> http://kdi.pnnl.gov/bios/baker.stm
> 
>  
> 
> From: Dimitrios Spiliotopoulos [mailto:dim...@gm...] 
> Sent: Friday, June 24, 2011 6:45 AM
> To: APBS Users Mailing List
> Subject: [Apbs-users] single-trajectory vs three-trajectory
> 
>  
> 
> Dear APBS users,
> 
> I have a question about the "single trajectory protocol" (STP, in what follows: the complex only is simulated, and the protein and the ligand structures are simply extracted from the complex structure by stripping the ligand and the protein, respectively) as opposed to the "three-trajectory protocol" (TTP: the simulations of the complex, the protein and the ligand are performed). 
> It is clear that the internal energy term zero out in the STP; I recall reading that this stands also for the entropic estimation, that zeroes out as the internal energy term does. I cannot find any reference about it. Am I wrong? If so, anybody stated this "officially"?
> 
> Thank you in advance!
> 
> Dimitrios Spiliotopoulos
> _________________________________________________________________________________________________
> Dulbecco Telethon Institute c/o DIBIT Scientific Institute
> Biomolecular NMR Laboratory, 1B4
> Via Olgettina 58, 20132 Milano (Italy)
> Tel     : 0039-0226434348/5622/3497/4922
> Fax    : 0039-0226434153
> Email : spi...@hs...; dim...@gm...
> Skype: dimitris3.16
> 
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