[gmx-users] Surface tension readings in NVT vs NPT simulations
David van der Spoel
spoel at xray.bmc.uu.se
Sat Mar 12 17:40:29 CET 2011
On 2011-03-12 17.36, Denny Frost wrote:
> It won't take zero with the berendsen thermostat, but I only wish to do
> weak coupling for now. Yes, I only specified the two values for
> semiisotropic. What I'm asking is will this setup only do z-pressure
> coupling?
http://manual.gromacs.org/current/online/mdp_opt.html#pc
>
> On Sat, Mar 12, 2011 at 9:32 AM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
> On 2011-03-12 17.28, Denny Frost wrote:
>
> No, it requires six, acutally, for aniisotropic coupling. I
> decided to
> use semi-isotropic coupling with the xy compressibilities set to
> 4.5e-15
> (it won't accept 0). This should keep the walls parallel to the
> z axis
> from moving and accomplish the same thing. Does this sound right?
>
> with semiisotropic you need only two values, with anisotropic either
> 3 or 6 values. Zero compressibility should work.
>
> On Sat, Mar 12, 2011 at 9:24 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 17.17, Denny Frost wrote:
>
> Thanks for answering that question about dispersion,
> that makes
> sense.
> Also, The values I currently get with NPT are around 58
> mN/m,
> while the
> average values I get for NVT are around 16 mN/m, but with a
> variance of
> nearly 100% of that value. I'm beginning to see why you
> only do
> pressure coupling in the z direction, but gromacs 4.5.3
> won't
> let you
> specify tau_p = 0. Any other way to do pressure coupling in
> just the z
> direction?
>
> check manual.
> maybe there is only one tau_p value.
>
> Denny
>
> On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost
> <dsfrost at cableone.net <mailto:dsfrost at cableone.net>
> <mailto:dsfrost at cableone.net <mailto:dsfrost at cableone.net>>
> <mailto:dsfrost at cableone.net <mailto:dsfrost at cableone.net>
> <mailto:dsfrost at cableone.net <mailto:dsfrost at cableone.net>>>> wrote:
>
> Is that using anisotropic pressure coupling?
>
>
> 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>
> <mailto: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>
> <mailto: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>>
> <mailto:aldi.asmadi at gmail.com <mailto:aldi.asmadi at gmail.com>
> <mailto:aldi.asmadi at gmail.com <mailto:aldi.asmadi at gmail.com>>>
> <mailto:aldi.asmadi at gmail.com <mailto:aldi.asmadi at gmail.com>
> <mailto:aldi.asmadi at gmail.com <mailto:aldi.asmadi at gmail.com>>
> <mailto: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>>
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> <mailto: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>
> <mailto:spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>>
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> <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>
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>
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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>
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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>
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> 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>
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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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