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?<br>
<br><div class="gmail_quote">On Sat, Mar 12, 2011 at 9:32 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 17.28, 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;">
No, it requires six, acutally, for aniisotropic coupling. I decided to<br>
use semi-isotropic coupling with the xy compressibilities set to 4.5e-15<br>
(it won't accept 0). This should keep the walls parallel to the z axis<br>
from moving and accomplish the same thing. Does this sound right?<br>
<br>
</blockquote></div>
with semiisotropic you need only two values, with anisotropic either 3 or 6 values. Zero compressibility should work.<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 Sat, Mar 12, 2011 at 9:24 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>
<br></div><div class="im">
On 2011-03-12 17.17, Denny Frost wrote:<br>
<br>
Thanks for answering that question about dispersion, that makes<br>
sense.<br>
Also, The values I currently get with NPT are around 58 mN/m,<br>
while the<br>
average values I get for NVT are around 16 mN/m, but with a<br>
variance of<br>
nearly 100% of that value. I'm beginning to see why you only do<br>
pressure coupling in the z direction, but gromacs 4.5.3 won't<br>
let you<br>
specify tau_p = 0. Any other way to do pressure coupling in<br>
just the z<br>
direction?<br>
<br>
check manual.<br>
maybe there is only one tau_p value.<br>
<br>
Denny<br>
<br>
On Sat, Mar 12, 2011 at 8:59 AM, Denny Frost<br>
<<a href="mailto:dsfrost@cableone.net" target="_blank">dsfrost@cableone.net</a> <mailto:<a href="mailto:dsfrost@cableone.net" target="_blank">dsfrost@cableone.net</a>><br></div><div class="im">
<mailto:<a href="mailto:dsfrost@cableone.net" target="_blank">dsfrost@cableone.net</a> <mailto:<a href="mailto:dsfrost@cableone.net" target="_blank">dsfrost@cableone.net</a>>>> wrote:<br>
<br>
Is that using anisotropic pressure coupling?<br>
<br>
<br>
On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel<br>
<<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>><br></div><div class="im">
<mailto:<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>
<br></div><div><div></div><div class="h5">
On 2011-03-12 16.45, Denny Frost wrote:<br>
<br>
I have run NPT simulations using isotropic and<br>
semiisotropic<br>
coupling<br>
with the same results. I have never done coupling<br>
in just<br>
one direction<br>
though, how do you do this?. I have never used<br>
Dispersion<br>
corrections.<br>
It seems to me that this would help, rather than<br>
hurt though<br>
since, as<br>
Aldi said, it will make the system closer to<br>
experimental<br>
values. I<br>
will give this a try and see what happens. My question<br>
still remains -<br>
why do NPT and NVT simulations give such different<br>
values<br>
for surface<br>
tension?<br>
Denny Frost<br>
<br>
<br>
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<br>
regards<br>
the average disperson constant per volume, which you<br>
probably do<br>
not have. E.g. in an ice/water surface dispersion<br>
correction may<br>
induce melting.<br>
<br>
The dispersion correction is *not* to bring your system<br>
closer<br>
to experiment but rather to correct for the use of a<br>
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>
<br>
<br>
On Sat, Mar 12, 2011 at 6:40 AM, aldi asmadi<br>
<<a href="mailto:aldi.asmadi@gmail.com" target="_blank">aldi.asmadi@gmail.com</a> <mailto:<a href="mailto:aldi.asmadi@gmail.com" target="_blank">aldi.asmadi@gmail.com</a>><br>
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<mailto:<a href="mailto:aldi.asmadi@gmail.com" target="_blank">aldi.asmadi@gmail.com</a> <mailto:<a href="mailto:aldi.asmadi@gmail.com" target="_blank">aldi.asmadi@gmail.com</a>><br></div></div>
<mailto:<a href="mailto:aldi.asmadi@gmail.com" target="_blank">aldi.asmadi@gmail.com</a> <mailto:<a href="mailto:aldi.asmadi@gmail.com" target="_blank">aldi.asmadi@gmail.com</a>>>>><div><div></div>
<div class="h5"><br>
wrote:<br>
<br>
David,<br>
<br>
I have a question that is still related to your<br>
reply.<br>
If the bulk<br>
liquid NPT and the interfacial liquid-vapor NVT<br>
simulations are<br>
performed using dispersion corrections to the<br>
pressure<br>
and energy,<br>
while the intefacial liquid-liquid NPAT<br>
simulation don't<br>
use any<br>
correction, can we say that all results are<br>
valid since<br>
we don't give<br>
the same treatment for all systems?<br>
<br>
In the NPT and NVT calculations, we apply<br>
corrections in<br>
order to<br>
reduce the discrepancy between the calculated and<br>
experimental<br>
properties (say density and surface tension) as<br>
small as<br>
possible.<br>
Here we have more confidence that our molecules in<br>
systems behave<br>
accordingly judging from the macroscopic values we<br>
obtain. Meanwhile,<br>
in the NPAT calculation, we don't use such<br>
correction<br>
meaning that the<br>
property (say interfacial tension) is expected to<br>
deviate more from<br>
the experimental value? This indicates that the<br>
system<br>
behaves<br>
differently in comparison to the same simulation<br>
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<br>
Spoel<br>
<<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>><br>
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<mailto:<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>><br>
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<br>
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<br>
have a lot of<br>
>> variation. I run NPT simulations on the exact same<br>
system and<br>
find the<br>
>> results show very little variation, but the values are<br>
far from<br>
>> experimental results. Does anyone know why this happens?<br>
>><br>
> Please be more specific. How do you do NPT simulations?<br>
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<br>
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>
> <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>><br>
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<br>
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