Re: [AMBER] To which ensemble does generalized Born trajectory fall?

From: David A Case <>
Date: Wed, 3 Oct 2012 07:56:17 -0400

On Tue, Oct 02, 2012, Sajeewa Pemasinghe wrote:
> I am hoping to run production MD with generalized Born solvation scheme
> I know that N (number of molecules), and T are constant. By default ntp=0
> so I am allowing the pressure to vary. What about the volume? Can I
> consider it to be constant or changing? The only ensemble I can think of
> inluding the resulting trajectory is , in N,V,T . This question might sound
> so naive but I really want to get my basics right.

Generalized Born simulations are run in non-periodic boundary conditions,
so there is no "volume" of the simulation; (or the effective volume is
infinite.) There is also no pressure per se. The properties of the
(implicit) water are probably closer to those of a constant pressure
solvent than of a constant volume one. (My reasoning: the solute could
change its shape and its partial molar volume without any penalty. This
is more like the situation with constant pressure than like constant
volume.) But if the small differences between ensembles are important to
you, don't use an implicit solvent model.

...good luck....dac

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Received on Wed Oct 03 2012 - 05:00:03 PDT
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