On 2011-03-12 17.36, Denny Frost wrote:
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?
http://manual.gromacs.org/current/online/mdp_opt.html#pc
On Sat, Mar 12, 2011 at 9:32 AM, David van der Spoel
<sp...@xray.bmc.uu.se <mailto:sp...@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
<sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
<mailto:sp...@xray.bmc.uu.se <mailto:sp...@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
<dsfr...@cableone.net <mailto:dsfr...@cableone.net>
<mailto:dsfr...@cableone.net <mailto:dsfr...@cableone.net>>
<mailto:dsfr...@cableone.net <mailto:dsfr...@cableone.net>
<mailto:dsfr...@cableone.net <mailto:dsfr...@cableone.net>>>> wrote:
Is that using anisotropic pressure coupling?
On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel
<sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
<mailto:sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>>
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<mailto:sp...@xray.bmc.uu.se <mailto:sp...@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
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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
<sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
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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.
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