[gmx-users] Pressure Question

[Johnny Lu]

I see. I'm using the V-rescaling thermostat in all simulations that I ran.
I don't think I will use NPT for production run.

I'm trying to get NVE production run in the end.
If I use NVT production run, I will try to account for the effect of the
thermostat (I'm not sure I can do that very well).


On Thu, Nov 6, 2014 at 10:47 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Note that using the Berendsen thermostat in Gromacs adds defects for no
> gain, compared with the Bussi v-rescale thermostat. The latter *is*
> Berendsen, plus a stochastic term that produces the right energy and
> velocity distributions (unlike Berendsen). I'd give serious consideration
> to rejecting a paper that used Gromacs and the Berendsen thermostat,
> particularly if they did not discuss why the known defects of Berendsen
> were acceptable for their work.
>
> Mark
>
> On Thu, Nov 6, 2014 at 4:18 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
> > That post in the amber mailing list was quite interesting. May be using a
> > weak berendsen thermostat in NVT is fine for them. Thanks for sharing
> that.
> >
> > On Thu, Nov 6, 2014 at 6:39 AM, 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. 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.
> > >
> > >
> > > 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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