I looked at that paper and there are no attempts to simulate liquid-gas
equilibrium at normal atmospheric pressure. That aside, what the authors
did instead is actually pretty mind-boggling: they replaced the droplet
with a cylinder by making the system periodic in the out-of-plane
direction.
This mailing list is probably not a great place for me to state my
opinion on this (terrible) paper, but one can indeed do what the authors
did. Just keep in mind that this is no longer a droplet, because the
surface not facing the substrate has been removed.
However, the good news is that you can indeed (partially) simulate
atmospheric pressure this way. To do this in Gromacs, simply use
'pcoupltype = semiisotropic' and supply a very low compressibility value
in the in-plane direction.
Alex
On 3/5/2017 12:27 AM, Rajorshi Paul wrote:
Thanks for your input. I am studying how a nano droplet spreads on a
substrate. I have created a four atomic layer thick FCC lattice surface on
which I have introduced water molecules. The entire system is placed inside
a box of dimensions 15 nm X 15 nm X 10 nm. The system is similar to the one
used in the following article:
https://www.cambridge.org/core/journals/journal-of-fluid-mechanics/article/div-classtitlea-molecular-view-of-tannerandaposs-law-molecular-dynamics-simulations-of-droplet-spreadingdiv/E4C863EE2CFE2E17B343D0AAE85D2BB4
I am interested in simulating normal atmospheric conditions in my study.
On 4 March 2017 at 23:30, Alex <nedoma...@gmail.com> wrote:
Once again, please describe your system in more detail, because this isn't
about Gromacs (which will correctly refuse pressure coupling for a finite,
deep-nanoscale system). It is about the meaning of where pressure comes
from in simulations and in reality.
In a realistic system "1 bar" would come from the air environment + any
water evaporation in equilibrium with the liquid phase of the droplet. Even
if you made your surface periodic, pressure coupling would have nothing to
do with your finite droplet -- it would be in vacuum. Consider this work,
for instance: http://www.nature.com/nmat/journal/v15/n1/abs/nmat4449.html
Alex
On 3/4/2017 11:17 PM, Rajorshi Paul wrote:
Hi Alex,
Like I mentioned, my system consists of a water nano drop on a substrate.
I
need my system to be at 1 bar and 298 K. Without pressure coupling, I am
unable to set the pressure to be at 1 bar.
On 4 March 2017 at 22:18, Alex <nedoma...@gmail.com> wrote:
1. Could you please provide a physical equivalent of a non-periodic NPT
system?
2. Why can't you turn off the barostat, like GMX is asking?
Alex
On 3/4/2017 8:40 PM, Rajorshi Paul wrote:
I am trying to simulate water nano droplet spreading on an FCC crystal
substrate. I have not implemented periodic boundary conditions as my
system
is non-periodic. But when I tried to equilibrate my system in NPT
ensemble,
the program gives me a warning that I should set pressure coupling as
"no".
Is it possible to run NPT equilibration in non-periodic system?
Thanks!
Raj.
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