[gmx-users] NPT equilibration without pbc

[Mark Abraham]

Hi,

People might find the approach at https://doi.org/10.1017/jfm.2015.517 more
rigorous!

Mark

On Mon, Mar 6, 2017 at 1:58 AM Rajorshi Paul <rajorshipaul.iitkgp at gmail.com>
wrote:

> Thanks Alex for the suggestion!!
>
> On 5 March 2017 at 01:49, Alex <nedomacho at gmail.com> wrote:
>
> > 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-tanneran
> >> daposs-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 <nedomacho at 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/jou
> >>> rnal/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 <nedomacho at 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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> >>>>>
> >>>>>
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> >>
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>
> --
> *Rajorshi Paul *
> B.Tech. (Hons.), Gold Medallist (IIT Kharagpur)
> First year Master of Science student
> Mechanical Engineering Department
> University of Alberta
> Edmonton, Alberta
> Canada.
> Office: NINT 6-17
> Email: rajorshipaul.iitkgp at gmail.com
> Phone: +1 780 782 4744 <+1%20780-782-4744>
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