Dear David, Vitaly and all, Thanks for the thoughts/comments. There are no partial charges on the carbons in this sheet. (Sorry if there was any confusion about this).
I used gromacs_4.5.5 version for these simulations. I also did increase the graphene sheet size to 10 nm x 10 nm and the box size to have 4142 water molecules. Initially the drop is placed about 3-4 nm away from the graphene sheet. In 600 ps the drop moves towards the sheet (forming something that looks like a pillar of water) and begins to spread on the sheet. The setup itself is placed in a 20 nm x 20 nm x 20 nm box. So both big sheet, and big box do not seem to help. The interesting part is I have another set of simulations with silica surface. The partial charges are turned off to make it hydrophobic. In this case the droplet remains a droplet. The mdp files are the same - I am using PME and NVT system with the drop and sheet coupled to different thermostats. The silica surface is frozen (so t_ref = 0 for the sheet). I have tested this system for gromacs 4.0.5, and 4.5.5. In both cases it remains a droplet. The only difference in the two is that in case of silica surface the surface is periodic, while graphene is a finite size sheet. Does this make such a big difference? Thoughts, comments, suggestions welcome! thanks all, Sapna On Sun, Apr 21, 2013 at 6:39 AM, Dr. Vitaly Chaban <vvcha...@gmail.com>wrote: > Yes, the water droplet should remain a droplet on graphene. > > Since you have a droplet, I assume you have much vacuum in the system. I > would not use PME for such system, but would rather "compensate" it by > using larger cutoffs. > > If you need a simple advice, it is -- enlarge the box to avoid any > interactions, which you would not have had in real experiment. > > I also expect a specific behavior, if your droplet is very small. > > Maybe, I would simulate this system without PBC at all. > > > Dr. Vitaly Chaban > > > > > > > > > I have a graphene like surface (carbons on a hexagonal lattice with zero > > partial charges and some LJ parameters) with a drop of water placed on > it. > > In principle, this is a hydrophobic surface and the drop should remain a > > droplet on it. However, surprisingly I am seeing that the drop is > spreading > > within a 1 ns of the simulation. In the past I have done some similar > > simulations (with a different structure but basically zero partial charge > > surface and LJ) on which the drop remains a drop. > > > > Does any body have any ideas of what I may be doing wrong? Pasted below > is > > my mdp and top file. Briefly, I am doing NVT simulation, PME for > > electrostatics, TIP3P water model, the surface is frozen and > intra-surface > > interactions are excluded, the cut-off distances are 1 nm, velocity > rescale > > thermostat (I tried both with the entire system coupled to the same > > thermostat and with sheet and water being coupled to different > > thermostats). > > Any suggestions are welcome. > > > > My analysis suggests this comes from the long range electrostatics > because > > we have tested the same thing in LAMMPS. When we turn off PPPM and use > > cut-off based Coulomb (~5 nm) in LAMMPS (yes now we have changed the > > software) we don't see the drop spreading. > > > > I have done so many simulations and to have this problem stumps me!! > Thanks > > for being helpful always. > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Sapna Sarupria Assistant Professor Department of Chemical and Biomolecular Engineering 128 Earle Hall Clemson University Clemson, SC 29634 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
