Wall atoms are virtual in the sense that they are just special Z-axis boundary conditions based on the integration of the LJ potential parameterized by the atom type, integraton model, and specified density of the "wall". The particles don't physically exist so you will not see them in VMD (because they are just a modification to the simulation box itself and don't show up in the coordinate file). I never got around to scripting pbctools to dynamically update the box outlines frame by frame either, but there is probably a way to do that. Theoretically, your walls would be seen where the lines are showing the top and bottom of the box :)
On 2012-11-01 10:37:43AM -0700, harshaljain950 wrote: > I have defined the wall by adding nwall option in my mdp file, I didn't > name it as 'carbon wall'. I just use this name to refer to this wall in > discussions > > Do you have any documentation or tutorial regarding implementation of > walls, I am in a great need of one as i am new to gromacs > > Thank you for replying > > > > > -- > View this message in context: > http://gromacs.5086.n6.nabble.com/are-wall-atoms-virtual-tp5002549p5002561.html > Sent from the GROMACS Users Forum mailing list archive at Nabble.com. > -- > 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
