[gmx-users] Surface tension readings in NVT vs NPT simulations
Denny Frost
dsfrost at cableone.net
Sat Mar 12 17:36:15 CET 2011
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?
On Sat, Mar 12, 2011 at 9:32 AM, David van der Spoel
<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>> 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>
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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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