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.iit...@gmail.com> wrote: > Thanks Alex for the suggestion!! > > On 5 March 2017 at 01:49, Alex <nedoma...@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 <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/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 <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. > >>>>>> > >>>>>> -- > >>>>>> > >>>>> Gromacs Users mailing list > >>>>> > >>>>> * Please search the archive at http://www.gromacs.org/Support > >>>>> /Mailing_Lists/GMX-Users_List before posting! > >>>>> > >>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>>>> > >>>>> * For (un)subscribe requests visit > >>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > >>>>> send a mail to gmx-users-requ...@gromacs.org. > >>>>> > >>>>> > >>>>> > >>>> -- > >>> Gromacs Users mailing list > >>> > >>> * Please search the archive at http://www.gromacs.org/Support > >>> /Mailing_Lists/GMX-Users_List before posting! > >>> > >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >>> > >>> * For (un)subscribe requests visit > >>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > >>> send a mail to gmx-users-requ...@gromacs.org. > >>> > >>> > >> > >> > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/Support > > /Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > -- > *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.iit...@gmail.com > Phone: +1 780 782 4744 <+1%20780-782-4744> > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.