For walls, the atoms in the wall are virtual. Remember that 9-3 LJ integratees over the volume behind the wall so you will have to set your atom density appropriately. Setting wall_density to 20/nm^3 for 9-3 wall leads to 20 carbon atoms per nm^3. That's not going to be totally solid, imo.
I am using 10-4 "2-D" walls to effect here: nwall = 2 wall_type = 10-4 wall_density = 5 5 wall_atomtype = CG331 CG331 wall_r_linpot = -1 wall_ewald_zfac = 3 ewald_geometry=3dc pbc=xy (CG331 is just a methyl group carbon specific to my forcefield). On 2012-04-05 10:08:02PM +0200, Huaichen(Bobby) Zhang wrote: > Dear all, > > I'm trying to simulate with pbc=xy and I need two walls. My settings are as > follows: > > pbc = xy > nwall = 2 > wall_atomtype = C C > wall_type = 9-3 > wall_r_linpot = -1 -1 > wall_density = 20 20 > wall_ewald_zfac = 3 > > The problem is how to define wall_atomtype in my topology file (top/itp)? A > want to have this solid carbon wall with 9-3 potential. Where in my top/itp > file can I define such atoms? This is my top file: > > #include "ffG53a6.itp" > #include "spc.itp" > > [ system ] > Pure Water with walls > > [ molecules ] > SOL 216 > > When I gmxdump the generated tpr file, I saw no C atoms are defined; and it > showed: > > wall_atomtype[0] = 2 > wall_atomtype[1] = 2 > > which corresponds to the hydrogen atom in my top file. And according to my > forcefield, the LJ parameters for H is 0,0. So there is basically no wall. > When I tried to simulate with this setting, the water molecules went out of > the box (in z direction) and moved far away. And according to g_energy, > there is no interaction energy between water and wall. So there indeed is > no wall. > > Can you help me with defining wall atom? If you have already finished any > tasks with this wall algorithm, can you kindly attach your topology files > to me? > > Soooooooooooooooooo many thanks!!!!!!!!!!!!!!!!! > > > -- > Huaichen(Bobby) ZHANG > > +31 648478172 > MSc Sustainable Energy Engineering > Royal Institute of Technology (Sweden) > Eindhoven University of Technology (Netherland) > -- > 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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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