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 -- 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.