Is that using anisotropic pressure coupling?<br><br><div class="gmail_quote">On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">On 2011-03-12 16.45, Denny Frost wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I have run NPT simulations using isotropic and semiisotropic coupling<br>
with the same results. I have never done coupling in just one direction<br>
though, how do you do this?. I have never used Dispersion corrections.<br>
It seems to me that this would help, rather than hurt though since, as<br>
Aldi said, it will make the system closer to experimental values. I<br>
will give this a try and see what happens. My question still remains -<br>
why do NPT and NVT simulations give such different values for surface<br>
tension?<br>
Denny Frost<br>
</blockquote>
<br></div>
You don't give any values so it is hard to judge.<br>
- NVT may have completely wrong pressure<br>
- 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.<br>
<br>
The dispersion correction is *not* to bring your system closer to experiment but rather to correct for the use of a cut-off.<br>
<br>
- Coupling in one direction: specify e.g.<br>
ref-p = 0 0 1<br>
compressibility = 0 0 4e-5<br>
tau_p = 0 0 5<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<br>
On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi <<a href="mailto:aldi.asmadi@gmail.com" target="_blank">aldi.asmadi@gmail.com</a><br></div><div class="im">
<mailto:<a href="mailto:aldi.asmadi@gmail.com" target="_blank">aldi.asmadi@gmail.com</a>>> wrote:<br>
<br>
David,<br>
<br>
I have a question that is still related to your reply. If the bulk<br>
liquid NPT and the interfacial liquid-vapor NVT simulations are<br>
performed using dispersion corrections to the pressure and energy,<br>
while the intefacial liquid-liquid NPAT simulation don't use any<br>
correction, can we say that all results are valid since we don't give<br>
the same treatment for all systems?<br>
<br>
In the NPT and NVT calculations, we apply corrections in order to<br>
reduce the discrepancy between the calculated and experimental<br>
properties (say density and surface tension) as small as possible.<br>
Here we have more confidence that our molecules in systems behave<br>
accordingly judging from the macroscopic values we obtain. Meanwhile,<br>
in the NPAT calculation, we don't use such correction meaning that the<br>
property (say interfacial tension) is expected to deviate more from<br>
the experimental value? This indicates that the system behaves<br>
differently in comparison to the same simulation conducted with<br>
correction?<br>
<br>
Many thanks,<br>
Aldi<br>
<br>
<br>
On Sat, Mar 12, 2011 at 11:44 AM, David van der Spoel<br></div><div class="im">
<<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <mailto:<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a>>> wrote:<br>
> On 2011-03-12 06.09, Denny Frost wrote:<br>
>><br>
>> I am running MD simulations on Liquid/Liquid interfaces and<br>
measuring<br>
>> the interfacial tension between them. I have found that the<br>
readings in<br>
>> NVT simulations are close to experimental values, but have a lot of<br>
>> variation. I run NPT simulations on the exact same system and<br>
find the<br>
>> results show very little variation, but the values are far from<br>
>> experimental results. Does anyone know why this happens?<br>
>><br>
> Please be more specific. How do you do NPT simulations? This may<br>
influence<br>
> the result. To get good result I would suggest to do pressure<br>
coupling only<br>
> in the normal direction and to turn off dispersion corrections to the<br>
> pressure.<br>
><br>
> --<br>
> David van der Spoel, Ph.D., Professor of Biology<br>
> Dept. of Cell & Molec. Biol., Uppsala University.<br>
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br></div>
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</div></blockquote><div><div></div><div class="h5">
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><br>
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