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

Denny Frost dsfrost at cableone.net
Sat Mar 12 17:17:11 CET 2011 

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?
Denny

On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost <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
> > 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>> 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>> 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>
>>>
>>>    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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