On Sat, May 5, 2012 at 7:27 PM, Za Pour <[email protected]> wrote: > Dear gmx users > I am simulation a system including carbon nanotube+water.I have done these > things: > However as I looked into the nvt.gro I realized that the cylindrical shape > of carbon nanotube > has been changed.I am not sure what I have done is correct or not?and how > to keep nanotube cylindrical ? any help would be really appreciated. > Best regards
I had a similar issue, but I modeled the CNT carbon atoms as opls_147, trying not to change the parameters too much, so I kept the bond lengths, angles and force constants untouched. I noticed that removing the [ dihedrals ] section from the resulting topology significantly reduced the tube deformation. Since g_x2top doesn't generate impropers and a CNT has no rotable bonds, these dihedrals are spurious, anyway. Also, do your tubes have open ends? If you can afford to have periodic tubes, so that the box z length is a multiple of the tube unit cell and the tube ends are bonded through the box wall, it seems much more stable. Or you could try capped tubes. -- Elton Carvalho Tel.: +55 11 3091-6985/6922 Dept Física dos Materiais e Mecânica Instituto de Física Universidade de São Paulo P.O. Box 66318 - 05314-970 São Paulo-SP, Brazil -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
