[gmx-users] Surface tension readings in NVT vs NPT simulations
David van der Spoel
spoel at xray.bmc.uu.se
Sat Mar 12 17:17:05 CET 2011
On 2011-03-12 16.59, Denny Frost wrote:
> Is that using anisotropic pressure coupling?
>
yes.
just try it
> On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
> On 2011-03-12 16.45, Denny Frost wrote:
>
> I have run NPT simulations using isotropic and semiisotropic
> coupling
> with the same results. I have never done coupling in just one
> direction
> though, how do you do this?. I have never used Dispersion
> corrections.
> It seems to me that this would help, rather than hurt though
> since, as
> Aldi said, it will make the system closer to experimental values. I
> will give this a try and see what happens. My question still
> remains -
> why do NPT and NVT simulations give such different values for
> surface
> tension?
> Denny Frost
>
>
> You don't give any values so it is hard to judge.
> - NVT may have completely wrong pressure
> - Dispersion correction assumes a homogeneous system as regards the
> average disperson constant per volume, which you probably do not
> have. E.g. in an ice/water surface dispersion correction may induce
> melting.
>
> The dispersion correction is *not* to bring your system closer to
> experiment but rather to correct for the use of a cut-off.
>
> - Coupling in one direction: specify e.g.
> ref-p = 0 0 1
> compressibility = 0 0 4e-5
> tau_p = 0 0 5
>
>
> On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi
> <aldi.asmadi at gmail.com <mailto:aldi.asmadi at gmail.com>
> <mailto:aldi.asmadi at gmail.com <mailto:aldi.asmadi at gmail.com>>>
> wrote:
>
> David,
>
> I have a question that is still related to your reply. If
> the bulk
> liquid NPT and the interfacial liquid-vapor NVT simulations are
> performed using dispersion corrections to the pressure and
> energy,
> while the intefacial liquid-liquid NPAT simulation don't use any
> correction, can we say that all results are valid since we
> don't give
> the same treatment for all systems?
>
> In the NPT and NVT calculations, we apply corrections in
> order to
> reduce the discrepancy between the calculated and experimental
> properties (say density and surface tension) as small as
> possible.
> Here we have more confidence that our molecules in systems
> behave
> accordingly judging from the macroscopic values we obtain.
> Meanwhile,
> in the NPAT calculation, we don't use such correction
> meaning that the
> property (say interfacial tension) is expected to deviate
> more from
> the experimental value? This indicates that the system behaves
> differently in comparison to the same simulation conducted with
> correction?
>
> Many thanks,
> Aldi
>
>
> On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>> wrote:
> > On 2011-03-12 06.09, Denny Frost wrote:
> >>
> >> I am running MD simulations on Liquid/Liquid interfaces and
> measuring
> >> the interfacial tension between them. I have found that the
> readings in
> >> NVT simulations are close to experimental values, but have a
> lot of
> >> variation. I run NPT simulations on the exact same system and
> find the
> >> results show very little variation, but the values are far from
> >> experimental results. Does anyone know why this happens?
> >>
> > Please be more specific. How do you do NPT simulations? This may
> influence
> > the result. To get good result I would suggest to do pressure
> coupling only
> > in the normal direction and to turn off dispersion
> corrections to the
> > pressure.
> >
> > --
> > David van der Spoel, Ph.D., Professor of Biology
> > Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> > spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>
>
> http://folding.bmc.uu.se
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> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
> spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
> http://folding.bmc.uu.se
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--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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