Re: [gmx-users] NPT equilibration without pbc
Thanks Alex for the suggestion!! On 5 March 2017 at 01:49, Alex 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 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 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. >>>>> >>>>> >>>>> >
Re: [gmx-users] NPT equilibration without pbc
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 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 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. > -- *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.
Re: [gmx-users] NPT equilibration without pbc
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 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. > -- *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.
[gmx-users] NPT equilibration without pbc
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.
[gmx-users] Creating an FCC lattice surface in GROMACS
Hi, I need to create a tethered FCC lattice surface in GROMACS. Is there any way of doing this directly in GROMACS? Is there any other software that can be used for the same and imported into GROMACS? 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.
