Maybe I didn't put it clearly. My intention is to simulate a protein confined in a box, and the problem is that I don't know how to define a boundary, or a wall, in GROMACS.
2008/10/10 Omer Markovitch <[EMAIL PROTECTED]> > Boundary should not "precisely" be around the protein, otherwise some parts > of the protein would "feel" other parts via the boundary. > In general, if you apply periodic boundary conditions (PBC), take the > dimensions as such so the protein would NOT feel the PBC. > > Say you have an unfolded protein (or a MD during which a protein unfolds) > whose length is about 20 Angstroms, and you use no explicit solvent. You > might not want to take the dimension of the box to be smaller they, say, 40 > Angstroms. > Its just an example. > > Omer. > > Koby Levy research group, > Weizmann Institute of Science. > http://www.weizmann.ac.il/sb/faculty_pages/Levy/ > > > On Fri, Oct 10, 2008 at 11:03, Lee Soin <[EMAIL PROTECTED]> wrote: > >> But the problem is: how to define a boundary? >> > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Sun Li Department of Physics Nanjing University, China
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