Hi Kester, Do you have experimental data on the behaviour of 2000 or 6000 or 10000 water molecules on a sheet of graphene? Do you _know_ it's wrong behaviour? If yes, then, given that the water forms a droplet in vacuum, even if above the graphene sheet, you know the water behaviour itself is sort of correct. I would be most suspicious of the water-graphene interactions. Where did those parameters come from? Do they account for increased electron density above the plane because of all the pi-orbitals?
Cheers, Tsjerk On Tue, Sep 2, 2014 at 8:24 AM, Kester Wong <kester2...@ibs.re.kr> wrote: > Dear gmx-users, > > > I am modelling a water droplet using a water box model, and have > encountered unrealistic behaviour of equilibrating water on graphene, using > GRAPPA force field in GROMACS 5.0. > > The box size is about 30x30x15 nm. Structure-wise, the water models (2000, > 6000, and 10,000 water molecules) appear to be spreading like a flat > layer of solution, rather than a droplet. > > Additionally, for the 10,000 molecules on graphene, water droplet was > formed in vacuo above the surface. > > > I have posted some questions on GROMACS user list, however, I have yet to > receive any feedback. > > Could anyone please look at my .mdp parameter and the .xtc trajectory > files? I do not know what caused the spreading of water on graphene. > > > There are two parameter settings that I have used, they are labeled as > lincs-order=4 (larger temperature constant and time-step), and > lincs-order=8 (smaller temperature constant and time-step). > The starting configuration (pdb), trajectories (xtc), and parameter (mdp) > files are uploaded in my Google Drive: > > > > https://drive.google.com/folderview?id=0B7ym8d6G9-e2Tlh4VGNSaDhCbmc&usp=sharing > > > https://drive.google.com/folderview?id=0B7ym8d6G9-e2Rl9WaXNrUlVRa28&usp=sharing > > > https://drive.google.com/folderview?id=0B7ym8d6G9-e2bnFzbWN3VHVqbE0&usp=sharing > > > Please let me know if you need more information/files on the GRAPPA-based > calculations. > > Any help will be tremendously appreciated. > > > > Regards, > > Kester > > > -- > 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. > > -- Tsjerk A. Wassenaar, Ph.D. -- 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.