[gmx-users] Surface tension readings in NVT vs NPT simulations

David van der Spoel spoel at xray.bmc.uu.se
Sat Mar 12 17:32:17 CET 2011


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>> 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>>> 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>>> 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>>>>
>         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>>
>         <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 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>>
>         <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>>>
>
>
>         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>
>         <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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