[gmx-users] Pressure Question

[Mark Abraham]

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
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at http://www.gromacs.org/
> >> Support/Mailing_Lists/GMX-Users_List before posting!
> >>
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >> * For (un)subscribe requests visit
> >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> >> send a mail to gmx-users-request at gromacs.org.
> >>
> >
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>