On 2011-03-12 16.59, Denny Frost wrote:
Is that using anisotropic pressure coupling?
yes.
just try it
On Sat, Mar 12, 2011 at 8:55 AM, David van der Spoel
<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
<aldi.asm...@gmail.com <mailto:aldi.asm...@gmail.com>
<mailto:aldi.asm...@gmail.com <mailto:aldi.asm...@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
<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 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.
> sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
<mailto:sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>>
http://folding.bmc.uu.se
> --
> gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before
posting!
> Please don't post (un)subscribe requests to the list. Use the www
interface
> or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>
http://folding.bmc.uu.se
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
sp...@xray.bmc.uu.se http://folding.bmc.uu.se
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
