[gmx-users] Pressure Question

[Mark Abraham]

On Thu, Nov 6, 2014 at 12:39 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> I was not offended by the suggestion. With a sufficiently large number of
> water molecules, the protein would behave in the same way, under all three
> ensembles.
> Barostat and thermostat are artificial in some way.


Biochemistry takes place in the NPT ensemble... NVT and NPT are different
from NVE, but that doesn't make them artificial. Implementing such
algorithms correctly is more tricky, however.

At least, even the
> diffusion coefficient is different in a force field paper that used both
> NVE and NVT. Langevin thermostat destroys some momentum transfer.
>
> This is my first paper, and I don't know if the reviewer will be fine if I
> report that my simulation has an average pressure of 11 bar with error 0.5
> bar.


That would concern me, slightly more than the fact that you have a single
simulation upon which to draw conclusions. Average pressure > 1 in a
fixed-volume ensemble means the system wants to change volume (get larger?
I forget the convention). Why not do some NPT to find a volume it
presumably likes better, and do another run? If the results are different,
then you need more runs to find out what's going on. If the results are the
same, then you've added weight to your conclusions.

Mark

On Thu, Nov 6, 2014 at 5:34 AM, Téletchéa Stéphane <
> stephane.teletchea at univ-nantes.fr> wrote:
>
> > Le 06/11/2014 06:16, Antonio Baptista a écrit :
> >
> >>
> >> In particular, the virial-based "instantaneous pressure" (call it P')
> >> computed in simulations has its ensemble average equal to the
> thermodynamic
> >> pressure P (check any good book on molecular simulation). But, as others
> >> already pointed out, this P' is well-known to show extremelly large
> >> fluctuations, meaning that its average computed from the simulation has
> >> usually a very large statistical spread. In other words, although the
> >> ensemble average of P' is strictly equal to P, its simulation average
> is a
> >> random variable that often shows large deviations from P (especially for
> >> short simulations). To get an idea of what is an acceptable error for
> the
> >> average of P', you may look at its distribution histogram in the NPT
> >> simulation.
> >>
> >
> > Dear Antonio,
> >
> > Sorry if my message sound "aggressive" when I talked about "totally
> > irrevelevant", I will clarify my thoughts.
> >
> > From a theoretical point of view, you are right, each ensemble is
> > accessible.
> >
> > From a biological point of view, though, the concept of fixing the volume
> > is less reasonable:
> > we live at constant pressure and temperature, and also at tighly
> > controlled pH, and salt concentrations.
> >
> > The volume varies though, as you feel it when the weather is getting hot
> > or cold.
> >
> > My point was exactly what your are telling in a more formal way than me:
> > "this P' is well-known to show extremely large fluctuations"
> >
> > Well, digging a bit more on my "feeling", I also found opposite arguments
> > on the AMBER mailing list,
> > like here: http://archive.ambermd.org/201103/0431.html
> >
> > So I'll got back again on my research and adjust my "mind" on the actual
> > bleeding edge simulations
> > taking into account all the recent code and force fields progresses.
> >
> > Best,
> >
> > Stéphane
> >
> > --
> > Team Protein Design In Silico
> > UFIP, UMR 6286 CNRS,
> > UFR Sciences et Techniques,
> > 2, rue de la Houssinière, Bât. 25,
> > 44322 Nantes cedex 03, France
> > Tél : +33 251 125 636
> > Fax : +33 251 125 632
> > http://www.ufip.univ-nantes.fr/ - http://www.steletch.org
> >
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