[gmx-users] Pressure Question

[Johnny Lu]

If the problem of using a 11 bar simulation is as big as the problem of
drawing conclusion from a single simulation, I guess I have to get a
pressure closer to 1 bar. Thanks.

On Thu, Nov 6, 2014 at 10:55 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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
>> > >>
>> > >> --
>> > >> 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.
>> >
>> --
>> 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.
>>
>
>